There's nothing that leaps out at me as being wrong - but syntax checking is the job of the parser (grompp) and logic checking can only be done by you. To do that, I would proceed slowly, demonstrating that small chunks of the force field can be used to generate results you can validate against something external (e.g. experiment, or a reference implementation of the force field). Don't just grab your simulation system and assume everything works!
Mark On Mon, Jan 28, 2013 at 7:35 AM, S. Alireza Bagherzadeh < s.a.bagherzade...@gmail.com> wrote: > Dear gmx-users, > > I am simulating a system in which I have a force field that is not included > in gromacs forcefields. > > So, I decided to construct my own force field in a sub-directory of my > actual > run. > > I read chapter 5 of gromacs 4.5.4 user manual (pgs. 107-139) and I prepared > the following files. > Below I am copying the content of a few sample files as well as my topology > file. > > I appreciate it if you could take a look and advise me whether anything is > missing, wrong or incomplete. > > Best regards, > > *{topol.top}:* > ; Topology for methane hydrate between silica surfaces in contact with > water and gas > > #include > > "/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/forcefield.itp" > > > ;Hydrate > ;----------------------------------------------- > ; water topology - hydrate phase > #include > > "/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/spce_hyd.itp" > > ; methane topology - large cages of hydrate phase > #include > > "/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/UAmethane_lc.itp" > > ; methane topology - small cages of hydrate phase > #include > > "/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/UAmethane_sc.itp" > ;------------------------------------------------ > > > ; water topology - liquid water > #include > > "/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/spce_liq.itp" > > > > ;Silica > ;---------------------------- > ; silica topology - bulk Si > #include > > "/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/SilicaLopez_Si.itp" > > ; silica topology - bulk O > #include > > "/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/SilicaLopez_Oi.itp" > > ; silica topology - surface O > #include > > "/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/SilicaLopez_Os.itp" > > ; silica topology - surface H > #include > > "/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/SilicaLopez_Hs.itp" > ;----------------------------- > > [ system ] > ; Name > Methane hydrate between 2 silica surfaces in contact with water and gas > > [ molecules ] > ; Compound #mols > HydrateW 2322 > HydG_sc 81 > HydG_lc 276 > SOL 3413 > Silica_Si 1848 > Silica_Oi 3360 > Silica_Os 672 > Silica_Hs 672 > > > > *SAMPLE FORCE FIELD FILES:* > > *{atomtypes.atp}:* > ;atmnm mass > Description > Reference > O 15.99940 ; water oxygen (hydrate & liquid phase), > tip4p-ice : > Ospc 15.99940 ; water oxygen (hydrate & liquid phase), > spc/e : > H 1.00800 ; water hydrogen (hydrate & liquid phase), > tip4p-ice : > Hspc 1.00800 ; water hydrogen (hydrate & liquid phase), > spc/e : > E 0.00000 ; dummy atom > (tip4p-ice) : > CH4 16.04300 ; United Atom methane (small/large cages of hydrate phase & > gas phase): > Si 28.08550 ; silica silicon (quartz > phase) : > Oi 15.99940 ; silica oxygen, bulk (inside) of the > crystal : > Os 15.99940 ; silica oxygen, surface of crystal (hydroxyl > group) : > Hs 1.00800 ; silica hydrogen, surface of crystal (hydroxyl > group) : > > *{ffnonbonded.itp}:* > [ atomtypes ] > ; name at.num mass charge ptype sigma(nm) epsilon(kj/mol) > H 1 1.0080 0.5897 A 0.00000e+00 0.00000e+00 ; > tip4p-ice: JCP 122,234511(2005) > Hspc 1 1.0080 0.4238 A 0.00000e+00 0.00000e+00 ; spce: > Hs 1 1.0080 0.3200 A 0.04000e+00 0.19246e+00 ; Lopez > et al: JPCB 110,2782 (2006) > CH4 6 16.0430 0.0000 A 0.36400e+00 1.36500e+00 ; United > Atom: JPC 87,4198(1983) > O 8 15.9994 0.0000 A 0.31668e+00 0.88217e+00 ; > tip4p-ice: JCP 122,234511(2005) > Ospc 8 15.9994 -0.8476 A 0.31656e+00 0.65017e+00 ; spc/e: > Oi 8 15.9994 -0.5300 A 0.31538e+00 0.63639e+00 ; Lopez > et al: JPCB 110,2782 (2006) > Os 8 15.9994 -0.6400 A 0.31538e+00 0.63639e+00 ; Lopez > et al: JPCB 110,2782 (2006) > Si 14 28.0855 1.0800 A 0.39200e+00 2.51040e+00 ; Lopez > et al: JPCB 110,2782 (2006) > E 0 0.0000 -1.1794 D 0.00000e+00 0.00000e+00 ; > tip4p-ice: JCP 122,234511(2005) > > *{forcefield.itp}:* > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 no 1.0 1.0 > ;MEANING > ;-------------------------------------------------------------- > ;L-J lorentz- > ;interaction berthelott > ;function combination > ; rule > > > #include "ffnonbonded.itp" > ;#include "ffbonded.itp" > > > *{SilicaLopez_Hs.itp}:* > ; methane topology - small cages of hydrate phase > [ moleculetype ] > ; Name nrexcl > Silica_Hs 1 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > 1 Hs 1 SiOH Hs 1 0.3200 1.008 > > > *{spce_hyd.itp}:* > ;spce water for Hydrate phase > ; > [ moleculetype ] > ; molname nrexcl > HydrateW 2 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass qtot > 1 Ospc 1 HYDW OWc 1 -0.8476 15.994 ; -0.8476 > 2 Hspc 1 HYDW HWc 1 0.4238 1.008 ; -0.4238 > 3 Hspc 1 HYDW HWc 1 0.4238 1.008 ; 0.0 > > [ constraints ] > ; i j func d (nm) > 1 2 1 0.10000 > 1 3 1 0.10000 > 2 3 1 0.16330 > > [ exclusions ] > 1 2 3 > 2 1 3 > 3 1 2 > > > *{UAmethane_gas.itp}:* > ; methane topology - gas phase > [ moleculetype ] > ; Name nrexcl > MethaneG 1 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > 1 CH4 1 GAS Cg 1 0.000 16.043 > > > > > > > > -- > S. Alireza Bagherzadeh > PhD Candidate > Dept. of Chem. & Bio. Eng. > University of BC > 2360 East Mall > Vancouver BC V6T1Z3 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists