Today's Topics:
1. Protein in vacum (Shima Arasteh)
2. Re: Inquiry about a completely user defined force field
(Mark Abraham)
------------------------------
Message: 2
Date: Mon, 28 Jan 2013 11:59:37 +0100
From: Mark Abraham <mark.j.abra...@gmail.com>
Subject: Re: [gmx-users] Inquiry about a completely user defined force
field
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<
camnumarsfd+wrwqrcpujipsvczypz8kujvaxd9h4ko51zlb...@mail.gmail.com>
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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
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End of gmx-users Digest, Vol 105, Issue 136
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