[gmx-users] Re: Inquiry about a completely user defined force field
Justin Lemkul
jalemkul at vt.edu
Thu Jan 31 22:57:56 CET 2013
On 1/31/13 1:57 PM, S. Alireza Bagherzadeh wrote:
> 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?
>
No, the .atp file is used by pdb2gmx. See the manual.
> 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.
>
Sorry, can't comment here. Without an .mdp file, it's hard to say anything.
Apologies if you posted it before and I missed it.
> 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).
>
Probably just a normal consequence of floating-point math. Check the topology
to be sure.
http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge
-Justin
>
> 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:
>> <
>> CAMNuMARsFD+WrWqrcPujiPsVcZYPZ8KuJVaxD9h4kO51zLBzrg at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> 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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>>
>>
>> ------------------------------
>>
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>> End of gmx-users Digest, Vol 105, Issue 136
>> *******************************************
>>
>
>
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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