9 The topology file is built following the |Gromacs| specification for a
10 molecular topology. A :ref:`top` file can be generated by
11 :ref:`pdb2gmx <gmx pdb2gmx>`. All possible entries in the topology file are
12 listed in :numref:`Tables %s <tab-topfile1>` and
13 :numref:`%s <tab-topfile2>`. Also tabulated are: all the units of
14 the parameters, which interactions can be perturbed for free energy
15 calculations, which bonded interactions are used by
16 :ref:`grompp <gmx grompp>` for generating exclusions, and which bonded
17 interactions can be converted to constraints by :ref:`grompp <gmx grompp>`.
19 .. |VCR| replace:: V\ :math:`^{(cr)}`
20 .. |WCR| replace:: W\ :math:`^{(cr)}`
21 .. |CRO| replace:: :math:`^{(cr)}`
22 .. |TREF| replace:: :numref:`Table %s <tab-topfile2>`
23 .. |AKJM| replace:: :math:`a~\mathrm{kJ~mol}^{-1}`
24 .. |KJN6| replace:: :math:`\mathrm{kJ~mol}^{-1}~\mathrm{nm}^{-6}`
25 .. |BNM| replace:: :math:`b~\mathrm{nm}^{-1}`
26 .. |C6LJ| replace:: :math:`c_6`
27 .. |STAR| replace:: :math:`^{(*)}`
28 .. |NREX| replace:: :math:`n_{ex}^{(nrexcl)}`
29 .. |QEMU| replace:: :math:`q` (e); :math:`m` (u)
30 .. |MQM| replace:: :math:`q,m`
34 .. table:: The :ref:`topology <top>` file.
36 +------------------------------------------------------------------------------------------------------------+
38 +===================+===========================+=====+====+=========================================+=======+
39 | interaction type | directive | # | f. | parameters | F. E. |
41 +-------------------+---------------------------+-----+----+-----------------------------------------+-------+
42 | *mandatory* | ``defaults`` | non-bonded function type; |
43 | | | combination rule\ |CRO|; |
44 | | | generate pairs (no/yes); |
45 | | | fudge LJ (); fudge QQ () |
46 +-------------------+---------------------------+------------------------------------------------------------+
47 | *mandatory* | ``atomtypes`` | atom type; m (u); q (e); particle type; |
49 +-------------------+---------------------------+------------------------------------------------------------+
50 | | ``bondtypes`` | (see |TREF|, directive ``bonds``) |
52 | | ``pairtypes`` | (see |TREF|, directive ``pairs``) |
54 | | ``angletypes`` | (see |TREF|, directive ``angles``) |
56 | | ``dihedraltypes``\ |STAR| | (see |TREF|, directive ``dihedrals``) |
58 | | ``constrainttypes`` | (see |TREF|, directive ``constraints``) |
59 +-------------------+---------------------------+-----+----+-------------------------------------------------+
60 | LJ | ``nonbond_params`` | 2 | 1 | |VCR| ; |WCR| |
62 | Buckingham | ``nonbond_params`` | 2 | 2 | |AKJM| ; |BNM|; |
63 | | | | | |C6LJ| (|KJN6|) |
64 +-------------------+---------------------------+-----+----+-------------------------------------------------+
68 +------------------------------------------------------------------------------------------------------------+
69 | Molecule definition(s) |
70 +===================+===========================+============================================================+
71 | *mandatory* | ``moleculetype`` | molecule name; |NREX| |
72 +-------------------+---------------------------+-----+----------------------------------------------+-------+
73 | *mandatory* | ``atoms`` | 1 | atom type; residue number; | type |
74 | | | | residue name; atom name; | |
75 | | | | charge group number; |QEMU| | |MQM| |
76 +-------------------+---------------------------+-----+----------------------------------------------+-------+
77 | intra-molecular interaction and geometry definitions as described in |TREF| |
78 +------------------------------------------------------------------------------------------------------------+
82 +-------------+---------------+------------------------------------+
84 +=============+===============+====================================+
85 | *mandatory* | ``system`` | system name |
86 +-------------+---------------+------------------------------------+
87 | *mandatory* | ``molecules`` | molecule name; number of molecules |
88 +-------------+---------------+------------------------------------+
92 +------------------------------+----------------------------------------------------+
93 | Inter-molecular interactions | |
94 +==============================+====================================================+
95 | *optional* | ``intermolecular_interactions`` |
96 +------------------------------+----------------------------------------------------+
97 | one or more bonded interactions as described in |TREF|, with two or more atoms, |
98 | no interactions that generate exclusions, no constraints, use global atom numbers |
99 +-----------------------------------------------------------------------------------+
103 '\# at' is the required number of atom type indices for this directive
104 'f. tp' is the value used to select this function type
105 'F. E.' indicates which of the parameters can be interpolated in free energy calculations
106 |CRO| the combination rule determines the type of LJ parameters, see
107 |STAR| for ``dihedraltypes`` one can specify 4 atoms or the inner (outer for improper) 2 atoms
108 |NREX| exclude neighbors :math:`n_{ex}` bonds away for non-bonded interactions
109 For free energy calculations, type, :math:`q` and :math:`m` or no parameters should be added
110 for topology 'B' (:math:`\lambda = 1`) on the same line, after the normal parameters.
112 .. |BZERO| replace:: :math:`b_0`
113 .. |KB| replace:: :math:`k_b`
114 .. |KDR| replace:: :math:`k_{dr}`
115 .. |NM2| replace:: (kJ mol\ :math:`^{-1}`\ nm\ :math:`^{-2}`
116 .. |NM4| replace:: (kJ mol\ :math:`^{-1}`\ nm\ :math:`^{-4}`
117 .. |DKJ| replace:: :math:`D` (kJ mol\ :math:`^{-1}`
118 .. |BETA| replace:: :math:`\beta` (nm\ :math:`^{-1}`
119 .. |C23| replace:: :math:`C_{i=2,3}` (kJ mol\ :math:`^{-1}\ nm\ :math:`^{-i}`
120 .. |BMM| replace:: :math:`b_m`
121 .. |GE0| replace:: :math:`\geq 0`
122 .. |KO| replace:: :math:`k`
123 .. |KJM| replace:: kJ mol\ :math:`^{-1}`
124 .. |LUU| replace:: low, up\ :math:`_1`,\ :math:`_2`
125 .. |MV| replace:: :math:`V`
126 .. |MW| replace:: :math:`W`
127 .. |QIJ| replace:: :math:`q_i`; :math:`q_j`
128 .. |THE0| replace:: :math:`\theta_0`
129 .. |KTHE| replace:: :math:`k_\theta`
130 .. |KJR2| replace:: kJ mol\ :math:`^{-1}`\ rad\ :math:`^{-2}`
131 .. |RN13| replace:: :math:`r_{13}`
132 .. |KUB| replace:: :math:`k_{UB}`
133 .. |C024| replace:: :math:`C_{i=0,1,2,3,4}`
134 .. |KJRI| replace:: kJ mol\ :math:`^{-1}`\ rad\ :math:`^{-i}`
135 .. |PHIS| replace:: :math:`\phi_s`
136 .. |PHI0| replace:: :math:`\phi_0`
137 .. |KPHI| replace:: :math:`k_\phi`
138 .. |PHIK| replace:: :math:`\phi,k`
139 .. |XI0| replace:: :math:`\xi_0`
140 .. |KXI| replace:: :math:`k_\xi`
141 .. |C0| replace:: :math:`C_0`
142 .. |C1| replace:: :math:`C_1`
143 .. |C2| replace:: :math:`C_2`
144 .. |C3| replace:: :math:`C_3`
145 .. |C4| replace:: :math:`C_4`
146 .. |C5| replace:: :math:`C_5`
147 .. |A0| replace:: :math:`a_0`
148 .. |A1| replace:: :math:`a_1`
149 .. |A2| replace:: :math:`a_2`
150 .. |A3| replace:: :math:`a_3`
151 .. |A4| replace:: :math:`a_4`
152 .. |DOH| replace:: :math:d_{\mbox{\sc oh}}`
153 .. |DHH| replace:: :math:d_{\mbox{\sc hh}}`
154 .. |AO| replace:: :math:`a`
155 .. |BO| replace:: :math:`b`
156 .. |CO| replace:: :math:`c`
157 .. |DO| replace:: :math:`d`
158 .. |KX| replace:: :math:`k_{x}`
159 .. |KY| replace:: :math:`k_{y}`
160 .. |KZ| replace:: :math:`k_{z}`
161 .. |GO| replace:: :math:`g`
162 .. |RO| replace:: :math:`r`
163 .. |DPHI| replace:: :math:`\Delta\phi`
164 .. |DIHR| replace:: :math:`k_{\mathrm{dihr}}`
165 .. |THET| replace:: :math:`\theta`
166 .. |NM| replace:: nm\ :math:`^{-1}`
167 .. |KC| replace:: :math:`k_c`
168 .. |THEK| replace:: :math:`\theta,k`
169 .. |R1E| replace:: :math:`r_{1e}`
170 .. |R2E| replace:: :math:`r_{2e}`
171 .. |R3E| replace:: :math:`r_{3e}`
172 .. |KRR| replace:: :math:`k_{rr'}`
173 .. |KRTH| replace:: :math:`k_{r\theta}`
174 .. |ALPH| replace:: :math:`\alpha`; |CO| (U nm\ :math:`^{\alpha}`
175 .. |UM1| replace:: U\ :math:`^{-1}`
179 .. table:: Details of ``[ moleculetype ]`` directives
181 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
182 | Name of interaction | Topology file directive | num. | func. | Order of parameters and their units | use in |
183 | | | atoms [1]_ | type [2]_ | | F.E.? [3]_ |
184 +====================================+============================+============+===========+=========================================================================+============+
185 | bond | ``bonds`` [4]_, [5]_ | 2 | 1 | |BZERO| (nm); |KB| |NM2| | all |
186 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
187 | G96 bond | ``bonds`` [4]_, [5]_ | 2 | 2 | |BZERO| (nm); |KB| |NM4| | all |
188 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
189 | Morse | ``bonds`` [4]_, [5]_ | 2 | 3 | |BZERO| (nm); |DKJ|; |BETA| | all |
190 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
191 | cubic bond | ``bonds`` [4]_, [5]_ | 2 | 4 | |BZERO| (nm); |C23| | |
192 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
193 | connection | ``bonds`` [4]_ | 2 | 5 | | |
194 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
195 | harmonic potential | ``bonds`` | 2 | 6 | |BZERO| (nm); |KB| |NM2| | all |
196 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
197 | FENE bond | ``bonds`` [4]_ | 2 | 7 | |BMM| (nm); |KB| |NM2| | |
198 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
199 | tabulated bond | ``bonds`` [4]_ | 2 | 8 | table number (|GE0|); |KO| |KJM| | |KO| |
200 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
201 | tabulated bond [6]_ | ``bonds`` | 2 | 9 | table number (|GE0|); |KO| |KJM| | |KO| |
202 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
203 | restraint potential | ``bonds`` | 2 | 10 | |LUU| (nm); |KDR| (|NM2|) | all |
204 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
205 | extra LJ or Coulomb | ``pairs`` | 2 | 1 | |MV| [7]_; |MW| [7]_ | all |
206 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
207 | extra LJ or Coulomb | ``pairs`` | 2 | 2 | fudge QQ (); |QIJ| (e), |MV| [7]_; |MW| [7]_ | |
208 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
209 | extra LJ or Coulomb | ``pairs_nb`` | 2 | 1 | |QIJ| (e); |MV| [7]_; |MW| [7]_ | |
210 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
211 | angle | ``angles`` [5]_ | 3 | 1 | |THE0| (deg); |KTHE| (|KJR2|) | all |
212 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
213 | G96 angle | ``angles`` [5]_ | 3 | 2 | |THE0| (deg); |KTHE| (|KJM|) | all |
214 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
215 | cross bond-bond | ``angles`` | 3 | 3 | |R1E|, |R2E| (nm); |KRR| (|NM2|) | |
216 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
217 | cross bond-angle | ``angles`` | 3 | 4 | |R1E|, |R2E|, |R3E| (nm); |KRTH| (|NM2|) | |
218 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
219 | Urey-Bradley | ``angles`` [5]_ | 3 | 5 | |THE0| (deg); |KTHE| (|KJR2|); |RN13| (nm); |KUB| (|NM2|) | all |
220 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
221 | quartic angle | ``angles`` [5]_ | 3 | 6 | |THE0| (deg); |C024| (|KJRI|) | |
222 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
223 | tabulated angle | ``angles`` | 3 | 8 | table number (|GE0|); |KO| (|KJM|) | |KO| |
224 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
225 | | restricted | | | | | |
226 | | bending potential | ``angles`` | 3 | 10 | |THE0| (deg); |KTHE| (|KJM|) | |
227 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
228 | proper dihedral | ``dihedrals`` | 4 | 1 | |PHIS| (deg); |KPHI| (|KJM|); multiplicity | |PHIK| |
229 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
230 | improper dihedral | ``dihedrals`` | 4 | 2 | |XI0| (deg); |KXI| (|KJR2|) | all |
231 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
232 | Ryckaert-Bellemans dihedral | ``dihedrals`` | 4 | 3 | |C0|, |C1|, |C2|, |C3|, |C4|, |C5| (|KJM|) | all |
233 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
234 | periodic improper dihedral | ``dihedrals`` | 4 | 4 | |PHIS| (deg); |KPHI| (|KJM|); multiplicity | |PHIK| |
235 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
236 | Fourier dihedral | ``dihedrals`` | 4 | 5 | |C1|, |C2|, |C3|, |C4|, |C5| (|KJM|) | all |
237 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
238 | tabulated dihedral | ``dihedrals`` | 4 | 8 | table number (|GE0|); |KO| (|KJM|) | |KO| |
239 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
240 | proper dihedral (multiple) | ``dihedrals`` | 4 | 9 | |PHIS| (deg); |KPHI| (|KJM|); multiplicity | |PHIK| |
241 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
242 | restricted dihedral | ``dihedrals`` | 4 | 10 | |PHI0| (deg); |KPHI| (|KJM|) | |
243 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
244 | combined bending-torsion potential | ``dihedrals`` | 4 | 11 | |A0|, |A1|, |A2|, |A3|, |A4| (|KJM|) | |
245 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
246 | exclusions | ``exclusions`` | 1 | | one or more atom indices | |
247 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
248 | constraint | ``constraints`` [4]_ | 2 | 1 | |BZERO| (nm) | all |
249 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
250 | constraint [6]_ | ``constraints`` | 2 | 2 | |BZERO| (nm) | all |
251 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
252 | SETTLE | ``settles`` | 1 | 1 | |DOH|, |DHH| (nm) | |
253 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
254 | 2-body virtual site | ``virtual_sites2`` | 3 | 1 | |AO| () | |
255 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
256 | 3-body virtual site | ``virtual_sites3`` | 4 | 1 | |AO|, |BO| () | |
257 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
258 | 3-body virtual site (fd) | ``virtual_sites3`` | 4 | 2 | |AO| (); |DO| (nm) | |
259 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
260 | 3-body virtual site (fad) | ``virtual_sites3`` | 4 | 3 | |THET| (deg); |DO| (nm) | |
261 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
262 | 3-body virtual site (out) | ``virtual_sites3`` | 4 | 4 | |AO|, |BO| (); |CO| (|NM|) | |
263 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
264 | 4-body virtual site (fdn) | ``virtual_sites4`` | 5 | 2 | |AO|, |BO| (); |CO| (nm) | |
265 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
266 | N-body virtual site (COG) | ``virtual_sitesn`` | 1 | 1 | one or more constructing atom indices | |
267 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
268 | N-body virtual site (COM) | ``virtual_sitesn`` | 1 | 2 | one or more constructing atom indices | |
269 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
270 | N-body virtual site (COW) | ``virtual_sitesn`` | 1 | 3 | | one or more pairs consisting of | |
271 | | | | | | constructing atom index and weight | |
272 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
273 | position restraint | ``position_restraints`` | 1 | 1 | |KX|, |KY|, |KZ| (|NM2|) | all |
274 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
275 | flat-bottomed position restraint | ``position_restraints`` | 1 | 2 | |GO|, |RO| (nm), |KO| (|NM2|) | |
276 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
277 | distance restraint | ``distance_restraints`` | 2 | 1 | type; label; |LUU| (nm); weight () | |
278 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
279 | dihedral restraint | ``dihedral_restraints`` | 4 | 1 | |PHI0| (deg); |DPHI| (deg); |DIHR| (|KJR2|) | all |
280 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
281 | orientation restraint | ``orientation_restraints`` | 2 | 1 | exp.; label; |ALPH|; obs. (U); weight (|UM1|) | |
282 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
283 | angle restraint | ``angle_restraints`` | 4 | 1 | |THE0| (deg); |KC| (|KJM|); multiplicity | |THEK| |
284 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
285 | angle restraint (z) | ``angle_restraints_z`` | 2 | 1 | |THE0| (deg); |KC| (|KJM|); multiplicity | |THEK| |
286 +------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
289 The required number of atom indices for this directive
292 The index to use to select this function type
295 Indicates which of the parameters can be interpolated in free energy calculations
298 This interaction type will be used by :ref:`grompp <gmx grompp>` for generating exclusions
301 This interaction type can be converted to constraints by :ref:`grompp <gmx grompp>`
304 The combination rule determines the type of LJ parameters, see
307 No connection, and so no exclusions, are generated for this interaction
309 Description of the file layout:
311 - Semicolon (;) and newline characters surround comments
313 - On a line ending with :math:`\backslash` the newline character is
316 - Directives are surrounded by ``[`` and ``]``
318 - The topology hierarchy (which must be followed) consists of three
321 - the parameter level, which defines certain force-field
322 specifications (see :numref:`Table %s <tab-topfile1>`)
324 - the molecule level, which should contain one or more molecule
325 definitions (see :numref:`Table %s <tab-topfile2>`)
327 - the system level, containing only system-specific information
328 (``[ system ]`` and ``[ molecules ]``)
330 - Items should be separated by spaces or tabs, not commas
332 - Atoms in molecules should be numbered consecutively starting at 1
334 - Atoms in the same charge group must be listed consecutively
336 - The file is parsed only once, which implies that no forward
337 references can be treated: items must be defined before they can be
340 - Exclusions can be generated from the bonds or overridden manually
342 - The bonded force types can be generated from the atom types or
345 - It is possible to apply multiple bonded interactions of the same type
348 - Descriptive comment lines and empty lines are highly recommended
350 - Starting with |Gromacs| version 3.1.3, all directives at the parameter
351 level can be used multiple times and there are no restrictions on the
352 order, except that an atom type needs to be defined before it can be
353 used in other parameter definitions
355 - If parameters for a certain interaction are defined multiple times
356 for the same combination of atom types the last definition is used;
357 starting with |Gromacs| version 3.1.3 :ref:`grompp <gmx grompp>` generates
358 a warning for parameter redefinitions with different values
360 - Using one of the ``[ atoms ]``,
361 ``[ bonds ]``, ``[ pairs ]``,
362 ``[ angles ]``, etc. without having used
363 ``[ moleculetype ]`` before is meaningless and generates
366 - Using ``[ molecules ]`` without having used
367 ``[ system ]`` before is meaningless and generates a
370 - After ``[ system ]`` the only allowed directive is
373 - Using an unknown string in ``[ ]`` causes all the data
374 until the next directive to be ignored and generates a warning
376 Here is an example of a topology file, ``urea.top``:
381 ; Example topology file
383 ; The force-field files to be included
384 #include "amber99.ff/forcefield.itp"
391 1 C 1 URE C 1 0.880229 12.01000 ; amber C type
392 2 O 1 URE O 2 -0.613359 16.00000 ; amber O type
393 3 N 1 URE N1 3 -0.923545 14.01000 ; amber N type
394 4 H 1 URE H11 4 0.395055 1.00800 ; amber H type
395 5 H 1 URE H12 5 0.395055 1.00800 ; amber H type
396 6 N 1 URE N2 6 -0.923545 14.01000 ; amber N type
397 7 H 1 URE H21 7 0.395055 1.00800 ; amber H type
398 8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
410 ; ai aj ak al funct definition
425 [ position_restraints ]
426 ; you wouldn't normally use this for a molecule like Urea,
427 ; but we include it here for didactic purposes
429 1 1 1000 1000 1000 ; Restrain to a point
430 2 1 1000 0 1000 ; Restrain to a line (Y-axis)
431 3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)
433 [ dihedral_restraints ]
434 ; ai aj ak al type phi dphi fc
438 ; Include TIP3P water topology
439 #include "amber99/tip3p.itp"
449 Here follows the explanatory text.
451 **#include “amber99.ff/forcefield.itp” :** this includes
452 the information for the force field you are using, including bonded and
453 non-bonded parameters. This example uses the AMBER99 force field, but
454 your simulation may use a different force field. :ref:`grompp <gmx grompp>`
455 will automatically go and find this file and copy-and-paste its content.
456 That content can be seen in
457 ``share/top/amber99.ff/forcefield.itp}``, and it
466 ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
469 #include "ffnonbonded.itp"
470 #include "ffbonded.itp"
472 The two ``#define`` statements set up the conditions so that
473 future parts of the topology can know that the AMBER 99 force field is
478 - ``nbfunc`` is the non-bonded function type. Use 1 (Lennard-Jones) or 2
481 - ``comb-rule`` is the number of the combination rule (see :ref:`nbpar`).
483 - ``gen-pairs`` is for pair generation. The default is
484 ‘no’, *i.e.* get 1-4 parameters from the pairtypes list. When
485 parameters are not present in the list, stop with a fatal error.
486 Setting ‘yes’ generates 1-4 parameters that are not present in the
487 pair list from normal Lennard-Jones parameters using
490 - ``fudgeLJ`` is the factor by which to multiply
491 Lennard-Jones 1-4 interactions, default 1
493 - ``fudgeQQ`` is the factor by which to multiply
494 electrostatic 1-4 interactions, default 1
496 - :math:`N` is the power for the repulsion term in a 6-\ :math:`N`
497 potential (with nonbonded-type Lennard-Jones only), starting with
498 |Gromacs| version 4.5, :ref:`grompp <gmx mdrun>` also reads and applies
499 :math:`N`, for values not equal to 12 tabulated interaction functions
500 are used (in older version you would have to use user tabulated
503 **Note** that ``gen-pairs``, ``fudgeLJ``,
504 ``fudgeQQ``, and :math:`N` are optional.
505 ``fudgeLJ`` is only used when generate pairs is set to
506 ‘yes’, and ``fudgeQQ`` is always used. However, if you want
507 to specify :math:`N` you need to give a value for the other parameters
510 Then some other ``#include`` statements add in the large
511 amount of data needed to describe the rest of the force field. We will
512 skip these and return to ``urea.top``. There we will see
514 **[ moleculetype ] :** defines the name of your molecule
515 in this :ref:`top` and nrexcl = 3 stands for excluding
516 non-bonded interactions between atoms that are no further than 3 bonds
519 **[ atoms ] :** defines the molecule, where
520 ``nr`` and ``type`` are fixed, the rest is user
521 defined. So ``atom`` can be named as you like,
522 ``cgnr`` made larger or smaller (if possible, the total
523 charge of a charge group should be zero), and charges can be changed
526 **[ bonds ] :** no comment.
528 **[ pairs ] :** LJ and Coulomb 1-4 interactions
530 **[ angles ] :** no comment
532 **[ dihedrals ] :** in this case there are 9 proper
533 dihedrals (funct = 1), 3 improper (funct = 4) and no Ryckaert-Bellemans
534 type dihedrals. If you want to include Ryckaert-Bellemans type dihedrals
535 in a topology, do the following (in case of *e.g.* decane):
540 ; ai aj ak al funct c0 c1 c2
544 In the original implementation of the potential for
545 alkanes \ :ref:`131 <refRyckaert78>` no 1-4 interactions were used, which means that in
546 order to implement that particular force field you need to remove the
547 1-4 interactions from the ``[ pairs ]`` section of your
548 topology. In most modern force fields, like OPLS/AA or Amber the rules
549 are different, and the Ryckaert-Bellemans potential is used as a cosine
550 series in combination with 1-4 interactions.
552 **[ position_restraints ] :** harmonically restrain the selected particles to reference
553 positions (:ref:`positionrestraint`). The reference positions are read
554 from a separate coordinate file by :ref:`grompp <gmx grompp>`.
556 **[ dihedral_restraints ] :** restrain selected dihedrals to a reference value. The
557 implementation of dihedral restraints is described in section
558 :ref:`dihedralrestraint` of the manual. The parameters specified in
559 the ``[dihedral_restraints]`` directive are as follows:
561 - ``type`` has only one possible value which is 1
563 - ``phi`` is the value of :math:`\phi_0` in :eq:`eqn. %s <eqndphi>` and
564 :eq:`eqn. %s <eqndihre>` of the manual.
566 - ``dphi`` is the value of :math:`\Delta\phi` in :eq:`eqn. %s <eqndihre>` of the
569 - ``fc`` is the force constant :math:`k_{dihr}` in :eq:`eqn. %s <eqndihre>` of the
572 **#include “tip3p.itp” :** includes a topology file that was already
573 constructed (see section :ref:`molitp`).
575 **[ system ] :** title of your system, user-defined
577 **[ molecules ] :** this defines the total number of (sub)molecules in your system
578 that are defined in this :ref:`top`. In this example file, it stands for 1
579 urea molecule dissolved in 1000 water molecules. The molecule type ``SOL``
580 is defined in the ``tip3p.itp`` file. Each name here must correspond to a
581 name given with ``[ moleculetype ]`` earlier in the topology. The order of the blocks of
582 molecule types and the numbers of such molecules must match the
583 coordinate file that accompanies the topology when supplied to :ref:`grompp <gmx grompp>`.
584 The blocks of molecules do not need to be contiguous, but some tools
585 (e.g. :ref:`genion <gmx genion>`) may act only on the first or last such block of a
586 particular molecule type. Also, these blocks have nothing to do with the
587 definition of groups (see sec. :ref:`groupconcept` and
588 sec. :ref:`usinggroups`).
595 If you construct a topology file you will use frequently (like the water
596 molecule, ``tip3p.itp``, which is already constructed for
597 you) it is good to make a ``molecule.itp`` file. This only
598 lists the information of one particular molecule and allows you to
599 re-use the ``[ moleculetype ]`` in multiple systems without
600 re-invoking :ref:`pdb2gmx <gmx pdb2gmx>` or manually copying and pasting. An
601 example ``urea.itp`` follows:
610 1 C 1 URE C 1 0.880229 12.01000 ; amber C type
612 8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
619 ; ai aj ak al funct definition
628 Using :ref:`itp` files results in a very short
634 ; Example topology file
636 ; The force field files to be included
637 #include "amber99.ff/forcefield.itp"
641 ; Include TIP3P water topology
642 #include "amber99/tip3p.itp"
655 A very powerful feature in |Gromacs| is the use of ``#ifdef``
656 statements in your :ref:`top` file. By making use of this
657 statement, and associated ``#define`` statements like were
658 seen in ``amber99.ff/forcefield.itp`` earlier,
659 different parameters for one molecule can be used in the same
660 :ref:`top` file. An example is given for TFE, where there is
661 an option to use different charges on the atoms: charges derived by De
662 Loof et al. :ref:`132 <refLoof92>` or by Van Buuren and
663 Berendsen \ :ref:`133 <refBuuren93a>`. In fact, you can use much of the
664 functionality of the C preprocessor, ``cpp``, because
665 :ref:`grompp <gmx grompp>` contains similar pre-processing functions to scan
666 the file. The way to make use of the ``#ifdef`` option is as
669 - either use the option ``define = -DDeLoof`` in the
670 :ref:`mdp` file (containing :ref:`grompp <gmx grompp>` input
671 parameters), or use the line ``#define DeLoof`` early in
672 your :ref:`top` or :ref:`itp` file; and
674 - put the ``#ifdef`` statements in your
675 :ref:`top`, as shown below:
685 ; nr type resnr residu atom cgnr charge mass
687 ; Use Charges from DeLoof
692 5 CH2 1 TFE CH2 1 0.25
693 6 OA 1 TFE OA 1 -0.65
696 ; Use Charges from VanBuuren
701 5 CH2 1 TFE CH2 1 0.26
702 6 OA 1 TFE OA 1 -0.55
708 6 7 1 1.000000e-01 3.138000e+05
709 1 2 1 1.360000e-01 4.184000e+05
710 1 3 1 1.360000e-01 4.184000e+05
711 1 4 1 1.360000e-01 4.184000e+05
712 1 5 1 1.530000e-01 3.347000e+05
713 5 6 1 1.430000e-01 3.347000e+05
716 This mechanism is used by :ref:`pdb2gmx <gmx pdb2gmx>` to implement optional position
717 restraints (:ref:`positionrestraint`) by ``#include``-ing an :ref:`itp` file
718 whose contents will be meaningful only if a particular ``#define`` is set
719 (and spelled correctly!)
721 Topologies for free energy calculations
722 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
724 Free energy differences between two systems, A and B, can be calculated
725 as described in sec. :ref:`fecalc`. Systems A and B are described by
726 topologies consisting of the same number of molecules with the same
727 number of atoms. Masses and non-bonded interactions can be perturbed by
728 adding B parameters under the ``[ atoms ]`` directive. Bonded interactions can be
729 perturbed by adding B parameters to the bonded types or the bonded
730 interactions. The parameters that can be perturbed are listed in
731 :numref:`Tables %s <tab-topfile1>` and :numref:`%s <tab-topfile2>`.
732 The :math:`\lambda`-dependence of the
733 interactions is described in section sec. :ref:`feia`. The bonded
734 parameters that are used (on the line of the bonded interaction
735 definition, or the ones looked up on atom types in the bonded type
736 lists) is explained in :numref:`Table %s <tab-topfe>`. In most cases, things should
737 work intuitively. When the A and B atom types in a bonded interaction
738 are not all identical and parameters are not present for the B-state,
739 either on the line or in the bonded types, :ref:`grompp <gmx grompp>` uses the A-state
740 parameters and issues a warning. For free energy calculations, all or no
741 parameters for topology B (:math:`\lambda = 1`) should be added on the
742 same line, after the normal parameters, in the same order as the normal
743 parameters. From |Gromacs| 4.6 onward, if :math:`\lambda` is treated as a
744 vector, then the ``bonded-lambdas`` component controls all bonded terms that
745 are not explicitly labeled as restraints. Restrain terms are controlled
746 by the ``restraint-lambdas`` component.
748 .. |NOT| replace:: :math:`-`
752 .. table:: The bonded parameters that are used for free energy topologies,
753 on the line of the bonded interaction definition or looked up
754 in the bond types section based on atom types. A and B indicate the
755 parameters used for state A and B respectively, + and |NOT| indicate
756 the (non-)presence of parameters in the topology, x indicates that
757 the presence has no influence.
759 +--------------------+---------------+---------------------------------+---------+
760 | B-state atom types | parameters | parameters in bonded types | |
761 + + +-----------------+---------------+ +
762 | all identical to | on line | A atom types | B atom types | message |
763 + +-------+-------+-------+---------+-------+-------+ +
764 | A-state atom types | A | B | A | B | A | B | |
765 +====================+=======+=======+=======+=========+=======+=======+=========+
766 | | +AB | |NOT| | x | x | | | |
767 | | +A | +B | x | x | | | |
768 | yes | |NOT| | |NOT| | |NOT| | |NOT| | | | error |
769 | | |NOT| | |NOT| | +AB | |NOT| | | | |
770 | | |NOT| | |NOT| | +A | +B | | | |
771 +--------------------+-------+-------+-------+---------+-------+-------+---------+
772 | | +AB | |NOT| | x | x | x | x | warning |
773 | | +A | +B | x | x | x | x | |
774 | | |NOT| | |NOT| | |NOT| | |NOT| | x | x | error |
775 | no | |NOT| | |NOT| | +AB | |NOT| | |NOT| | |NOT| | warning |
776 | | |NOT| | |NOT| | +A | +B | |NOT| | |NOT| | warning |
777 | | |NOT| | |NOT| | +A | x | +B | |NOT| | |
778 | | |NOT| | |NOT| | +A | x | + | +B | |
779 +--------------------+-------+-------+-------+---------+-------+-------+---------+
783 Below is an example of a topology which changes from 200 propanols to
784 200 pentanes using the GROMOS-96 force field.
789 ; Include force field parameters
790 #include "gromos43a1.ff/forcefield.itp"
797 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
798 1 H 1 PROP PH 1 0.398 1.008 CH3 0.0 15.035
799 2 OA 1 PROP PO 1 -0.548 15.9994 CH2 0.0 14.027
800 3 CH2 1 PROP PC1 1 0.150 14.027 CH2 0.0 14.027
801 4 CH2 1 PROP PC2 2 0.000 14.027
802 5 CH3 1 PROP PC3 2 0.000 15.035
805 ; ai aj funct par_A par_B
817 ; ai aj ak funct par_A par_B
823 ; ai aj ak al funct par_A par_B
824 1 2 3 4 1 gd_12 gd_17
825 2 3 4 5 1 gd_17 gd_17
835 Atoms that are not perturbed, ``PC2`` and
836 ``PC3``, do not need B-state parameter specifications, since
837 the B parameters will be copied from the A parameters. Bonded
838 interactions between atoms that are not perturbed do not need B
839 parameter specifications, as is the case for the last bond in the
840 example topology. Topologies using the OPLS/AA force field need no
841 bonded parameters at all, since both the A and B parameters are
842 determined by the atom types. Non-bonded interactions involving one or
843 two perturbed atoms use the free-energy perturbation functional forms.
844 Non-bonded interactions between two non-perturbed atoms use the normal
845 functional forms. This means that when, for instance, only the charge of
846 a particle is perturbed, its Lennard-Jones interactions will also be
847 affected when lambda is not equal to zero or one.
849 **Note** that this topology uses the GROMOS-96 force field, in which the
850 bonded interactions are not determined by the atom types. The bonded
851 interaction strings are converted by the C-preprocessor. The force-field
852 parameter files contain lines like:
856 #define gb_26 0.1530 7.1500e+06
858 #define gd_17 0.000 5.86 3
865 | The constraint force between two atoms in one molecule can be
866 calculated with the free energy perturbation code by adding a
867 constraint between the two atoms, with a different length in the A and
868 B topology. When the B length is 1 nm longer than the A length and
869 lambda is kept constant at zero, the derivative of the Hamiltonian
870 with respect to lambda is the constraint force. For constraints
871 between molecules, the pull code can be used, see sec. :ref:`pull`.
872 Below is an example for calculating the constraint force at 0.7 nm
873 between two methanes in water, by combining the two methanes into one
874 “molecule.” **Note** that the definition of a “molecule” in |Gromacs|
875 does not necessarily correspond to the chemical definition of a
876 molecule. In |Gromacs|, a “molecule” can be defined as any group of
877 atoms that one wishes to consider simultaneously. The added constraint
878 is of function type 2, which means that it is not used for generating
879 exclusions (see sec. :ref:`excl`). Note that the constraint free energy
880 term is included in the derivative term, and is specifically included
881 in the ``bonded-lambdas`` component. However, the free energy for changing
882 constraints is *not* included in the potential energy differences used
883 for BAR and MBAR, as this requires reevaluating the energy at each of
884 the constraint components. This functionality is planned for later
889 ; Include force-field parameters
890 #include "gromos43a1.ff/forcefield.itp"
897 ; nr type resnr residu atom cgnr charge mass
898 1 CH4 1 CH4 C1 1 0 16.043
899 2 CH4 1 CH4 C2 2 0 16.043
901 ; ai aj funct length_A length_B
904 #include "gromos43a1.ff/spc.itp"
918 Files with the :ref:`gro` file extension contain a molecular
919 structure in GROMOS-87 format. A sample piece is included below:
923 MD of 2 waters, reformat step, PA aug-91
925 1WATER OW1 1 0.126 1.624 1.679 0.1227 -0.0580 0.0434
926 1WATER HW2 2 0.190 1.661 1.747 0.8085 0.3191 -0.7791
927 1WATER HW3 3 0.177 1.568 1.613 -0.9045 -2.6469 1.3180
928 2WATER OW1 4 1.275 0.053 0.622 0.2519 0.3140 -0.1734
929 2WATER HW2 5 1.337 0.002 0.680 -1.0641 -1.1349 0.0257
930 2WATER HW3 6 1.326 0.120 0.568 1.9427 -0.8216 -0.0244
931 1.82060 1.82060 1.82060
933 This format is fixed, *i.e.* all columns are in a fixed position. If you
934 want to read such a file in your own program without using the |Gromacs|
935 libraries you can use the following formats:
938 ``“%5i%5s%5s%5i%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f”``
940 Or to be more precise, with title *etc.* it looks like this:
946 for (i=0; (i<natoms); i++) {
947 "%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n",
948 residuenr,residuename,atomname,atomnr,x,y,z,vx,vy,vz
950 "%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\n",
951 box[X][X],box[Y][Y],box[Z][Z],
952 box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]
955 ``(i5,2a5,i5,3f8.3,3f8.4)``
957 So ``confin.gro`` is the |Gromacs| coordinate file and is
958 almost the same as the GROMOS-87 file (for GROMOS users: when used with
959 ``ntx=7``). The only difference is the box for which |Gromacs|
960 uses a tensor, not a vector.