[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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