.. |C6LJ| replace:: :math:`c_6`
.. |STAR| replace:: :math:`^{(*)}`
.. |NREX| replace:: :math:`n_{ex}^{(nrexcl)}`
-.. |QEMU| replace:: :math:`q` (e); :math:`m` (u)
+.. |QEMU| replace:: :math:`q` (e); :math:`m` (u)
.. |MQM| replace:: :math:`q,m`
.. _tab-topfile1:
| | | generate pairs (no/yes); |
| | | fudge LJ (); fudge QQ () |
+-------------------+---------------------------+------------------------------------------------------------+
- | *mandatory* | ``atomtypes`` | atom type; m (u); q (e); particle type; |
+ | *mandatory* | ``atomtypes`` | atom type; m (u); q (e); particle type; |
| | | |VCR| ; |WCR| |
+-------------------+---------------------------+------------------------------------------------------------+
| | ``bondtypes`` | (see |TREF|, directive ``bonds``) |
| | | | | |C6LJ| (|KJN6|) |
+-------------------+---------------------------+-----+----+-------------------------------------------------+
-.. table::
+.. table::
+------------------------------------------------------------------------------------------------------------+
| Molecule definition(s) |
| no interactions that generate exclusions, no constraints, use global atom numbers |
+-----------------------------------------------------------------------------------+
-.. parsed-literal::
+- ``# at`` is the required number of atom type indices for this directive
+
+- ``f. tp`` is the value used to select this function type
+
+- ``F. E.`` indicates which of the parameters can be interpolated in free energy calculations
+
+- |CRO| the combination rule determines the type of LJ parameters, see :ref:`nbpar`
+
+- |STAR| for ``dihedraltypes`` one can specify 4 atoms or the inner (outer for improper) 2 atoms
+
+- |NREX| exclude neighbors :math:`n_{ex}` bonds away for non-bonded interactions
- '\# at' is the required number of atom type indices for this directive
- 'f. tp' is the value used to select this function type
- 'F. E.' indicates which of the parameters can be interpolated in free energy calculations
- |CRO| the combination rule determines the type of LJ parameters, see
- |STAR| for ``dihedraltypes`` one can specify 4 atoms or the inner (outer for improper) 2 atoms
- |NREX| exclude neighbors :math:`n_{ex}` bonds away for non-bonded interactions
- For free energy calculations, type, :math:`q` and :math:`m` or no parameters should be added
- for topology 'B' (:math:`\lambda = 1`) on the same line, after the normal parameters.
+- For free energy calculations, type, :math:`q` and :math:`m` or no parameters should be added for topology ``B`` (:math:`\lambda = 1`) on the same line, after the normal parameters.
.. |BZERO| replace:: :math:`b_0`
.. |KB| replace:: :math:`k_b`
.. |C23| replace:: :math:`C_{i=2,3}` (kJ mol\ :math:`^{-1}\ nm\ :math:`^{-i}`
.. |BMM| replace:: :math:`b_m`
.. |GE0| replace:: :math:`\geq 0`
-.. |KO| replace:: :math:`k`
+.. |KO| replace:: :math:`k`
.. |KJM| replace:: kJ mol\ :math:`^{-1}`
.. |LUU| replace:: low, up\ :math:`_1`,\ :math:`_2`
.. |MV| replace:: :math:`V`
.. |A2| replace:: :math:`a_2`
.. |A3| replace:: :math:`a_3`
.. |A4| replace:: :math:`a_4`
-.. |DOH| replace:: :math:d_{\mbox{\sc oh}}`
-.. |DHH| replace:: :math:d_{\mbox{\sc hh}}`
+.. |DOH| replace:: :math:`d_{\mbox{\sc oh}}`
+.. |DHH| replace:: :math:`d_{\mbox{\sc hh}}`
.. |AO| replace:: :math:`a`
.. |BO| replace:: :math:`b`
.. |CO| replace:: :math:`c`
.. table:: Details of ``[ moleculetype ]`` directives
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | Name of interaction | Topology file directive | num. | func. | Order of parameters and their units | use in |
+ | Name of interaction | Topology file directive | num. | func. | Order of parameters and their units | use in |
| | | atoms [1]_ | type [2]_ | | F.E.? [3]_ |
+====================================+============================+============+===========+=========================================================================+============+
- | bond | ``bonds`` [4]_, [5]_ | 2 | 1 | |BZERO| (nm); |KB| |NM2| | all |
+ | bond | ``bonds`` [4]_, [5]_ | 2 | 1 | |BZERO| (nm); |KB| |NM2| | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| G96 bond | ``bonds`` [4]_, [5]_ | 2 | 2 | |BZERO| (nm); |KB| |NM4| | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | Morse | ``bonds`` [4]_, [5]_ | 2 | 3 | |BZERO| (nm); |DKJ|; |BETA| | all |
+ | Morse | ``bonds`` [4]_, [5]_ | 2 | 3 | |BZERO| (nm); |DKJ|; |BETA| | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | cubic bond | ``bonds`` [4]_, [5]_ | 2 | 4 | |BZERO| (nm); |C23| | |
+ | cubic bond | ``bonds`` [4]_, [5]_ | 2 | 4 | |BZERO| (nm); |C23| | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | connection | ``bonds`` [4]_ | 2 | 5 | | |
+ | connection | ``bonds`` [4]_ | 2 | 5 | | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | harmonic potential | ``bonds`` | 2 | 6 | |BZERO| (nm); |KB| |NM2| | all |
+ | harmonic potential | ``bonds`` | 2 | 6 | |BZERO| (nm); |KB| |NM2| | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | FENE bond | ``bonds`` [4]_ | 2 | 7 | |BMM| (nm); |KB| |NM2| | |
+ | FENE bond | ``bonds`` [4]_ | 2 | 7 | |BMM| (nm); |KB| |NM2| | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| tabulated bond | ``bonds`` [4]_ | 2 | 8 | table number (|GE0|); |KO| |KJM| | |KO| |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| tabulated bond [6]_ | ``bonds`` | 2 | 9 | table number (|GE0|); |KO| |KJM| | |KO| |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | restraint potential | ``bonds`` | 2 | 10 | |LUU| (nm); |KDR| (|NM2|) | all |
+ | restraint potential | ``bonds`` | 2 | 10 | |LUU| (nm); |KDR| (|NM2|) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | extra LJ or Coulomb | ``pairs`` | 2 | 1 | |MV| [7]_; |MW| [7]_ | all |
+ | extra LJ or Coulomb | ``pairs`` | 2 | 1 | |MV| [7]_; |MW| [7]_ | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | extra LJ or Coulomb | ``pairs`` | 2 | 2 | fudge QQ (); |QIJ| (e), |MV| [7]_; |MW| [7]_ | |
+ | extra LJ or Coulomb | ``pairs`` | 2 | 2 | fudge QQ (); |QIJ| (e), |MV| [7]_; |MW| [7]_ | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | extra LJ or Coulomb | ``pairs_nb`` | 2 | 1 | |QIJ| (e); |MV| [7]_; |MW| [7]_ | |
+ | extra LJ or Coulomb | ``pairs_nb`` | 2 | 1 | |QIJ| (e); |MV| [7]_; |MW| [7]_ | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | angle | ``angles`` [5]_ | 3 | 1 | |THE0| (deg); |KTHE| (|KJR2|) | all |
+ | angle | ``angles`` [5]_ | 3 | 1 | |THE0| (deg); |KTHE| (|KJR2|) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | G96 angle | ``angles`` [5]_ | 3 | 2 | |THE0| (deg); |KTHE| (|KJM|) | all |
+ | G96 angle | ``angles`` [5]_ | 3 | 2 | |THE0| (deg); |KTHE| (|KJM|) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | cross bond-bond | ``angles`` | 3 | 3 | |R1E|, |R2E| (nm); |KRR| (|NM2|) | |
+ | cross bond-bond | ``angles`` | 3 | 3 | |R1E|, |R2E| (nm); |KRR| (|NM2|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | cross bond-angle | ``angles`` | 3 | 4 | |R1E|, |R2E|, |R3E| (nm); |KRTH| (|NM2|) | |
+ | cross bond-angle | ``angles`` | 3 | 4 | |R1E|, |R2E|, |R3E| (nm); |KRTH| (|NM2|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| Urey-Bradley | ``angles`` [5]_ | 3 | 5 | |THE0| (deg); |KTHE| (|KJR2|); |RN13| (nm); |KUB| (|NM2|) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | quartic angle | ``angles`` [5]_ | 3 | 6 | |THE0| (deg); |C024| (|KJRI|) | |
+ | quartic angle | ``angles`` [5]_ | 3 | 6 | |THE0| (deg); |C024| (|KJRI|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | tabulated angle | ``angles`` | 3 | 8 | table number (|GE0|); |KO| (|KJM|) | |KO| |
+ | tabulated angle | ``angles`` | 3 | 8 | table number (|GE0|); |KO| (|KJM|) | |KO| |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| | restricted | | | | | |
- | | bending potential | ``angles`` | 3 | 10 | |THE0| (deg); |KTHE| (|KJM|) | |
+ | | bending potential | ``angles`` | 3 | 10 | |THE0| (deg); |KTHE| (|KJM|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | proper dihedral | ``dihedrals`` | 4 | 1 | |PHIS| (deg); |KPHI| (|KJM|); multiplicity | |PHIK| |
+ | proper dihedral | ``dihedrals`` | 4 | 1 | |PHIS| (deg); |KPHI| (|KJM|); multiplicity | |PHIK| |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | improper dihedral | ``dihedrals`` | 4 | 2 | |XI0| (deg); |KXI| (|KJR2|) | all |
+ | improper dihedral | ``dihedrals`` | 4 | 2 | |XI0| (deg); |KXI| (|KJR2|) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | Ryckaert-Bellemans dihedral | ``dihedrals`` | 4 | 3 | |C0|, |C1|, |C2|, |C3|, |C4|, |C5| (|KJM|) | all |
+ | Ryckaert-Bellemans dihedral | ``dihedrals`` | 4 | 3 | |C0|, |C1|, |C2|, |C3|, |C4|, |C5| (|KJM|) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | periodic improper dihedral | ``dihedrals`` | 4 | 4 | |PHIS| (deg); |KPHI| (|KJM|); multiplicity | |PHIK| |
+ | periodic improper dihedral | ``dihedrals`` | 4 | 4 | |PHIS| (deg); |KPHI| (|KJM|); multiplicity | |PHIK| |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | Fourier dihedral | ``dihedrals`` | 4 | 5 | |C1|, |C2|, |C3|, |C4|, |C5| (|KJM|) | all |
+ | Fourier dihedral | ``dihedrals`` | 4 | 5 | |C1|, |C2|, |C3|, |C4|, |C5| (|KJM|) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| tabulated dihedral | ``dihedrals`` | 4 | 8 | table number (|GE0|); |KO| (|KJM|) | |KO| |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | proper dihedral (multiple) | ``dihedrals`` | 4 | 9 | |PHIS| (deg); |KPHI| (|KJM|); multiplicity | |PHIK| |
+ | proper dihedral (multiple) | ``dihedrals`` | 4 | 9 | |PHIS| (deg); |KPHI| (|KJM|); multiplicity | |PHIK| |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | restricted dihedral | ``dihedrals`` | 4 | 10 | |PHI0| (deg); |KPHI| (|KJM|) | |
+ | restricted dihedral | ``dihedrals`` | 4 | 10 | |PHI0| (deg); |KPHI| (|KJM|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | combined bending-torsion potential | ``dihedrals`` | 4 | 11 | |A0|, |A1|, |A2|, |A3|, |A4| (|KJM|) | |
+ | combined bending-torsion potential | ``dihedrals`` | 4 | 11 | |A0|, |A1|, |A2|, |A3|, |A4| (|KJM|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | exclusions | ``exclusions`` | 1 | | one or more atom indices | |
+ | exclusions | ``exclusions`` | 1 | | one or more atom indices | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | constraint | ``constraints`` [4]_ | 2 | 1 | |BZERO| (nm) | all |
+ | constraint | ``constraints`` [4]_ | 2 | 1 | |BZERO| (nm) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | constraint [6]_ | ``constraints`` | 2 | 2 | |BZERO| (nm) | all |
+ | constraint [6]_ | ``constraints`` | 2 | 2 | |BZERO| (nm) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | SETTLE | ``settles`` | 1 | 1 | |DOH|, |DHH| (nm) | |
+ | SETTLE | ``settles`` | 1 | 1 | |DOH|, |DHH| (nm) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| 1-body virtual site | ``virtual_sites1`` | 2 | 0 | | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | 2-body virtual site | ``virtual_sites2`` | 3 | 1 | |AO| () | |
+ | 2-body virtual site | ``virtual_sites2`` | 3 | 1 | |AO| () | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | 2-body virtual site (fd) | ``virtual_sites2`` | 3 | 2 | |DO| (nm) | |
+ | 2-body virtual site (fd) | ``virtual_sites2`` | 3 | 2 | |DO| (nm) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | 3-body virtual site | ``virtual_sites3`` | 4 | 1 | |AO|, |BO| () | |
+ | 3-body virtual site | ``virtual_sites3`` | 4 | 1 | |AO|, |BO| () | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | 3-body virtual site (fd) | ``virtual_sites3`` | 4 | 2 | |AO| (); |DO| (nm) | |
+ | 3-body virtual site (fd) | ``virtual_sites3`` | 4 | 2 | |AO| (); |DO| (nm) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | 3-body virtual site (fad) | ``virtual_sites3`` | 4 | 3 | |THET| (deg); |DO| (nm) | |
+ | 3-body virtual site (fad) | ``virtual_sites3`` | 4 | 3 | |THET| (deg); |DO| (nm) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | 3-body virtual site (out) | ``virtual_sites3`` | 4 | 4 | |AO|, |BO| (); |CO| (|NM|) | |
+ | 3-body virtual site (out) | ``virtual_sites3`` | 4 | 4 | |AO|, |BO| (); |CO| (|NM|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | 4-body virtual site (fdn) | ``virtual_sites4`` | 5 | 2 | |AO|, |BO| (); |CO| (nm) | |
+ | 4-body virtual site (fdn) | ``virtual_sites4`` | 5 | 2 | |AO|, |BO| (); |CO| (nm) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | N-body virtual site (COG) | ``virtual_sitesn`` | 1 | 1 | one or more constructing atom indices | |
+ | N-body virtual site (COG) | ``virtual_sitesn`` | 1 | 1 | one or more constructing atom indices | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | N-body virtual site (COM) | ``virtual_sitesn`` | 1 | 2 | one or more constructing atom indices | |
+ | N-body virtual site (COM) | ``virtual_sitesn`` | 1 | 2 | one or more constructing atom indices | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| N-body virtual site (COW) | ``virtual_sitesn`` | 1 | 3 | | one or more pairs consisting of | |
- | | | | | | constructing atom index and weight | |
+ | | | | | | constructing atom index and weight | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| position restraint | ``position_restraints`` | 1 | 1 | |KX|, |KY|, |KZ| (|NM2|) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | flat-bottomed position restraint | ``position_restraints`` | 1 | 2 | |GO|, |RO| (nm), |KO| (|NM2|) | |
+ | flat-bottomed position restraint | ``position_restraints`` | 1 | 2 | |GO|, |RO| (nm), |KO| (|NM2|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | distance restraint | ``distance_restraints`` | 2 | 1 | type; label; |LUU| (nm); weight () | |
+ | distance restraint | ``distance_restraints`` | 2 | 1 | type; label; |LUU| (nm); weight () | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | dihedral restraint | ``dihedral_restraints`` | 4 | 1 | |PHI0| (deg); |DPHI| (deg); |DIHR| (|KJR2|) | all |
+ | dihedral restraint | ``dihedral_restraints`` | 4 | 1 | |PHI0| (deg); |DPHI| (deg); |DIHR| (|KJR2|) | all |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| orientation restraint | ``orientation_restraints`` | 2 | 1 | exp.; label; |ALPH|; obs. (U); weight (|UM1|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | angle restraint | ``angle_restraints`` | 4 | 1 | |THE0| (deg); |KC| (|KJM|); multiplicity | |THEK| |
+ | angle restraint | ``angle_restraints`` | 4 | 1 | |THE0| (deg); |KC| (|KJM|); multiplicity | |THEK| |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | angle restraint (z) | ``angle_restraints_z`` | 2 | 1 | |THE0| (deg); |KC| (|KJM|); multiplicity | |THEK| |
+ | angle restraint (z) | ``angle_restraints_z`` | 2 | 1 | |THE0| (deg); |KC| (|KJM|); multiplicity | |THEK| |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
.. [1]
The required number of atom indices for this directive
-
+
.. [2]
The index to use to select this function type
-
+
.. [3]
Indicates which of the parameters can be interpolated in free energy calculations
-
+
.. [4]
This interaction type will be used by :ref:`grompp <gmx grompp>` for generating exclusions
-
+
.. [5]
This interaction type can be converted to constraints by :ref:`grompp <gmx grompp>`
-
+
.. [7]
- The combination rule determines the type of LJ parameters, see
-
+ The combination rule determines the type of LJ parameters, see :ref:`nbpar`
+
.. [6]
No connection, and so no exclusions, are generated for this interaction
8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
[ bonds ]
- 1 2
- 1 3
- 1 6
- 3 4
- 3 5
- 6 7
- 6 8
+ 1 2
+ 1 3
+ 1 6
+ 3 4
+ 3 5
+ 6 7
+ 6 8
- [ dihedrals ]
+ [ dihedrals ]
; ai aj ak al funct definition
- 2 1 3 4 9
- 2 1 3 5 9
- 2 1 6 7 9
- 2 1 6 8 9
- 3 1 6 7 9
- 3 1 6 8 9
- 6 1 3 4 9
- 6 1 3 5 9
-
- [ dihedrals ]
- 3 6 1 2 4
- 1 4 3 5 4
+ 2 1 3 4 9
+ 2 1 3 5 9
+ 2 1 6 7 9
+ 2 1 6 8 9
+ 3 1 6 7 9
+ 3 1 6 8 9
+ 6 1 3 4 9
+ 6 1 3 5 9
+
+ [ dihedrals ]
+ 3 6 1 2 4
+ 1 4 3 5 4
1 7 6 8 4
[ position_restraints ]
1 4 3 5 1 180 0 10
; Include TIP3P water topology
- #include "amber99/tip3p.itp"
+ #include "amber99.ff/tip3p.itp"
[ system ]
Urea in Water
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
- 1 2 3 4 3
+ 1 2 3 4 3
2 3 4 5 3
In the original implementation of the potential for
1 2
...
6 8
- [ dihedrals ]
+ [ dihedrals ]
; ai aj ak al funct definition
- 2 1 3 4 9
+ 2 1 3 4 9
...
- 6 1 3 5 9
- [ dihedrals ]
- 3 6 1 2 4
- 1 4 3 5 4
+ 6 1 3 5 9
+ [ dihedrals ]
+ 3 6 1 2 4
+ 1 4 3 5 4
1 7 6 8 4
Using :ref:`itp` files results in a very short
; nr type resnr residu atom cgnr charge mass
#ifdef DeLoof
; Use Charges from DeLoof
- 1 C 1 TFE C 1 0.74
- 2 F 1 TFE F 1 -0.25
- 3 F 1 TFE F 1 -0.25
- 4 F 1 TFE F 1 -0.25
- 5 CH2 1 TFE CH2 1 0.25
- 6 OA 1 TFE OA 1 -0.65
- 7 HO 1 TFE HO 1 0.41
+ 1 C 1 TFE C 1 0.74
+ 2 F 1 TFE F 1 -0.25
+ 3 F 1 TFE F 1 -0.25
+ 4 F 1 TFE F 1 -0.25
+ 5 CH2 1 TFE CH2 1 0.25
+ 6 OA 1 TFE OA 1 -0.65
+ 7 HO 1 TFE HO 1 0.41
#else
; Use Charges from VanBuuren
- 1 C 1 TFE C 1 0.59
- 2 F 1 TFE F 1 -0.2
- 3 F 1 TFE F 1 -0.2
- 4 F 1 TFE F 1 -0.2
- 5 CH2 1 TFE CH2 1 0.26
- 6 OA 1 TFE OA 1 -0.55
- 7 HO 1 TFE HO 1 0.3
+ 1 C 1 TFE C 1 0.59
+ 2 F 1 TFE F 1 -0.2
+ 3 F 1 TFE F 1 -0.2
+ 4 F 1 TFE F 1 -0.2
+ 5 CH2 1 TFE CH2 1 0.26
+ 6 OA 1 TFE OA 1 -0.55
+ 7 HO 1 TFE HO 1 0.3
#endif
[ bonds ]
; ai aj funct c0 c1
- 6 7 1 1.000000e-01 3.138000e+05
- 1 2 1 1.360000e-01 4.184000e+05
- 1 3 1 1.360000e-01 4.184000e+05
- 1 4 1 1.360000e-01 4.184000e+05
- 1 5 1 1.530000e-01 3.347000e+05
- 5 6 1 1.430000e-01 3.347000e+05
+ 6 7 1 1.000000e-01 3.138000e+05
+ 1 2 1 1.360000e-01 4.184000e+05
+ 1 3 1 1.360000e-01 4.184000e+05
+ 1 4 1 1.360000e-01 4.184000e+05
+ 1 5 1 1.530000e-01 3.347000e+05
+ 5 6 1 1.430000e-01 3.347000e+05
...
This mechanism is used by :ref:`pdb2gmx <gmx pdb2gmx>` to implement optional position
::
-
+
; Include force field parameters
#include "gromos43a1.ff/forcefield.itp"
5 CH3 1 PROP PC3 2 0.000 15.035
[ bonds ]
- ; ai aj funct par_A par_B
+ ; ai aj funct par_A par_B
1 2 2 gb_1 gb_26
2 3 2 gb_17 gb_26
3 4 2 gb_26 gb_26
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff