From: Szilard Pall Date: Wed, 29 Feb 2012 16:50:32 +0000 (+0100) Subject: Merge branch 'release-4-5-patches' into release-4-6 X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=379f5cb40751fc5ff39170a2c832d605c956fbce;p=alexxy%2Fgromacs.git Merge branch 'release-4-5-patches' into release-4-6 Also fixed uninitialized variable warning in pdb2top.c with gcc 4.3. Conflicts: share/html/online/mdp_opt.html Change-Id: I8e499a77a3ce71c2063f453348330e2aad38669b --- 379f5cb40751fc5ff39170a2c832d605c956fbce diff --cc share/html/online/mdp_opt.html index 3f40b3d9e2,84c6bf37b8..5333233517 --- a/share/html/online/mdp_opt.html +++ b/share/html/online/mdp_opt.html @@@ -522,8 -522,8 +522,8 @@@ The dielectric constant can be set to i

Generalized-Reaction-Field

Generalized reaction field with Coulomb cut-off rcoulomb, - where rcoulomb &ge rlist. + where rcoulomb ≥ rlist. -The dielectric constant beyond the cut-off is epsilon_rf. +The dielectric constant beyond the cut-off is epsilon-rf. The ionic strength is computed from the number of charged (i.e. with non zero charge) charge groups. The temperature for the GRF potential is set with @@@ -640,12 -640,12 +640,12 @@@ A value of 0 means infinity.

vdwtype:

Cut-off: Twin range cut-off's with neighbor list cut-off rlist and +; Twin range cut-offs with neighbor list cut-off rlist and VdW cut-off rvdw, - where rvdw &ge rlist.

Shift

The LJ (not Buckingham) potential is decreased over the whole -range and the forces decay smoothly to zero between rvdw_switch +range and the forces decay smoothly to zero between rvdw-switch and rvdw. The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rvdw to accommodate for the size of charge groups and diffusion between neighbor list @@@ -672,10 -672,10 +672,10 @@@ The function value at x=0 is n use LJ correction, make sure that rvdw corresponds to the cut-off in the user-defined function. When coulombtype is not set to User the values - for f and -f' are ignored.

+ for f and -f' are ignored. -

rvdw_switch: (0) [nm]

rvdw-switch: (0) [nm]

where to start switching the LJ potential

rvdw: (1) [nm]

@@@ -730,7 -730,7 +730,7 @@@ energy group pairs For ordinary Ewald the spacing times the box dimensions determines the highest magnitude to use in each direction. In all cases each direction can be overridden by entering a non-zero value for - fourier-n*. -fourier_n[xyz]. ++fourier-n[xyz]. For optimizing the relative load of the particle-particle interactions and the mesh part of PME it is useful to know that the accuracy of the electrostatics remains nearly constant @@@ -767,8 -767,8 +767,8 @@@ the slab height is usually ok and use this option. -

epsilon_surface: (0)

epsilon-surface: (0)

This controls the dipole correction to the Ewald summation in 3d. The +

This controls the dipole correction to the Ewald summation in 3D. The default value of zero means it is turned off. Turn it on by setting it to the value of the relative permittivity of the imaginary surface around your infinite system. Be careful - you shouldn't use this if you have free mobile charges in your system. @@@ -880,17 -880,17 +880,17 @@@ oscillations if you are starting from

pcoupltype:

isotropic: Isotropic pressure coupling with time constant tau_p [ps]. +; Isotropic pressure coupling with time constant tau-p [ps]. The compressibility and reference pressure are set with -compressibility [bar^-1] and ref_p [bar], one +compressibility [bar^-1] and ref-p [bar], one value is needed.
semiisotropic: Pressure coupling which is isotropic in the x and y direction, - but different in the z direction. +; Pressure coupling which is isotropic in the x and y direction, + but different in the z direction. This can be useful for membrane simulations. - 2 values are needed for x/y and z directions respectively.

anisotropic

Idem, but 6 values are needed for xx, yy, zz, xy/yx, xz/zx and yz/zy +

Idem, but 6 values are needed for xx, yy, zz, xy/yx, xz/zx and yz/zy components, respectively. When the off-diagonal compressibilities are set to zero, a rectangular box will stay rectangular. @@@ -898,14 -898,14 +898,14 @@@ Beware that anisotropic scaling can lea of the simulation box.

surface-tension

Surface tension coupling for surfaces parallel to the xy-plane. - Uses normal pressure coupling for the z-direction, while the surface tension - is coupled to the x/y dimensions of the box. + Uses normal pressure coupling for the z-direction, while the surface tension + is coupled to the x/y dimensions of the box. -The first ref_p value is the reference surface tension times +The first ref-p value is the reference surface tension times the number of surfaces [bar nm], - the second value is the reference z-pressure [bar]. + the second value is the reference z-pressure [bar]. The two compressibility [bar^-1] values are the compressibility - in the x/y and z direction respectively. - The value for the z-compressibility should be reasonably accurate since it + in the x/y and z direction respectively. + The value for the z-compressibility should be reasonably accurate since it influences the convergence of the surface-tension, it can also be set to zero to have a box with constant height.

@@@ -1107,18 -1107,18 +1107,18 @@@ solvent. This is especially useful for

Walls

nwall: 0: When set to 1 there is a wall at z=0, when set to 2 - there is also a wall at z=z-box. Walls can only be used with pbc=xy. +; When set to 1 there is a wall at z=0, when set to 2 -there is also a wall at z=z_box. Walls can only be used with pbc=xy. ++there is also a wall at z=z-box. Walls can only be used with pbc=xy. When set to 2 pressure coupling and Ewald summation can be used (it is usually best to use semiisotropic pressure coupling with - the x/y compressibility set to 0, as otherwise the surface area will change). + the x/y compressibility set to 0, as otherwise the surface area will change). -Walls interact wit the rest of the system through an optional wall_atomtype. +Walls interact wit the rest of the system through an optional wall-atomtype. Energy groups wall0 and wall1 (for nwall=2) are added automatically to monitor the interaction of energy groups with each wall. The center of mass motion removal will be turned - off in the z-direction.
wall_atomtype:
wall-atomtype:: the atom type name in the force field for each wall. By (for example) defining a special wall atom type in the topology with its own combination rules, this allows for independent tuning of the interaction diff --cc src/kernel/pdb2top.c index fc66165d76,535c2e53f9..5169ffefd1 --- a/src/kernel/pdb2top.c +++ b/src/kernel/pdb2top.c @@@ -1349,12 -1345,20 +1345,20 @@@ void match_atomnames_with_rtp(t_restp r } } - void gen_cmap(t_params *psb, t_restp *restp, int natoms, t_atom atom[], char **aname[], int nres) + #define NUM_CMAP_ATOMS 5 + static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms, gmx_residuetype_t rt) { - int residx,i,ii,j,k; - atom_id ai,aj,ak,al,am; - const char *ptr; - + int residx,i,j,k; + const char *ptr; + int natoms = atoms->nr; + t_atom *atom = atoms->atom; + char ***aname = atoms->atomname; + t_resinfo *resinfo = atoms->resinfo; + int nres = atoms->nres; + gmx_bool bAddCMAP; + atom_id cmap_atomid[NUM_CMAP_ATOMS]; - int cmap_chainnum, this_residue_index; ++ int cmap_chainnum=-1, this_residue_index; + if (debug) ptr = "cmap"; else