[gmx-users] Inquiry about a completely user defined force field

[S. Alireza Bagherzadeh]

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