[gmx-users] Inquiry about a completely user defined force field
Mark Abraham
mark.j.abraham at gmail.com
Mon Jan 28 11:59:37 CET 2013
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.bagherzadeh.h at 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
> --
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