[gmx-users] SPC/E water for Charmm ff implementation

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jul 21 13:47:25 CEST 2011

On 21/07/2011 4:26 PM, E. Nihal Korkmaz wrote:
> Thanks but I already checked the literature. What I want to do is, to 
> be able to trace down the parameters in the nonbonded file like it can 
> be done for any version of gromos. There are slight changes among 
> different force fields and I'd like to be able to find that. When I 
> find where it reads spc/e parameters for c27, i want to play with the 
> parameters that's why i am asking the file read.

Anything that's not found in spce.itp is looked up from ffbonded.itp or 
ffnonbonded.itp. I can't think of a single case where the charges in 
ffnonbonded.itp are used, so there's probably no reason to expect them 
to be correct. You should satisfy yourself that GROMACS is implementing 
the correct form of SPC/E found in the primary literature. However, 
since CHARMM was not parameterized with SPC/E, there probably is no 
particular correct form to use.


> Thanks,
> Nihal
> On Wed, Jul 20, 2011 at 11:05 PM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 21/07/2011 12:59 PM, E. Nihal Korkmaz wrote:
>         Dear all,
>         I was trying to see the LJ parameters for SPC/E water in
>         Charmm27.ff implementation in Gromacs. In the ffnonbonded.itp
>         file i can see parameters for TIP3P, TIP4P, SPC but not for
>         SPC/E. Does SPC/E use the same parameters with SPC? (but the
>         charges listed in the ffnonbonded.itp is different than the
>         ones listed in spce.itp)
>     Why not check out the primary literature? Search GROMACS manual
>     for SPC, follow the reference link for the relevant citation.
>     Mark
>     -- 
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> Elif Nihal Korkmaz
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone:  608-265-3644
> Email: korkmaz at wisc.edu <mailto:korkmaz at wisc.edu>

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