[gmx-users] Re: Inquiry about a completely user defined force field
S. Alireza Bagherzadeh
s.a.bagherzadeh.h at gmail.com
Thu Jan 31 19:57:42 CET 2013
Dear Dr.Abraham,
Thank you for taking the time to look at my files.
However, I have one question remained in my mind:
Where is the "atomtypes.atp" used in the force field?
I suspect that this file is only for clarification for the user in
order to eliminate/minimize
confusion and this file is not read by the program. Am I correct?
I would also like to ask you for any insight on why in my system the tempera
ture keeps increasing linearly with time under NVE ensemble (even up to
unrealistic T of 550K)? I have verified this force filed with DL_POLY and
my system showed a gradual temperature decrease which is the correct
physical behavior of the system.
One clue which might be useful is that even though when I hand-calculate
the total charge of my system to be zero, the gormacs warns me that my
system has the total charge of 0.000108. Could this be the reason? Do you
have any suggestions for me to solve this potential problem? (I am not
using gromacs in double-precision mode).
Best regards,
Alireza
>
> 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.abraham at gmail.com>
> Subject: Re: [gmx-users] Inquiry about a completely user defined force
> field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
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> CAMNuMARsFD+WrWqrcPujiPsVcZYPZ8KuJVaxD9h4kO51zLBzrg at 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.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
> >
> >
> >
> >
> >
>
> > --
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> End of gmx-users Digest, Vol 105, Issue 136
> *******************************************
>
--
S. Alireza Bagherzadeh
PhD Candidate
Dept. of Chem. & Bio. Eng.
University of BC
2360 East Mall
Vancouver BC V6T1Z3
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