[gmx-users] GROMOS with SPC/E water?

Berk Hess gmx3 at hotmail.com
Thu Nov 13 16:20:18 CET 2008


Force fields have usually been parametrized with one specific water model.
For all GROMOS force fields this water model is SPC.
The people behind GROMOS would recommend you not to use any other
water model.

I have tested thermodynamic properties of GROMOS with SPC and SPC/E
and I would say that SPC/E actually performs slightly better than SPC
(and SPC/E is a better model for water than SPC), see:

For configuration (gro) file, it does not matter much which starting configuration
you use, since you anyhow have to (re)equilibrate the solvent after you
solvate your solute. The differences in conformation between all 3-site
water models are minimal and will dissappear after a few hundred steps.


> Date: Thu, 13 Nov 2008 20:47:46 +0530
> From: suman at sscu.iisc.ernet.in
> To: gmx-users at gromacs.org
> Subject: [gmx-users] GROMOS with SPC/E water?
> Dear all,
> I am a little confused with the statement in the pdb2gmx man page: "with
> GROMOS we recommend SPC, with OPLS, TIP4P: spc , spce ..."
> What is the specific reason behind this recommendation? What kind of
> problems there might be if I want to use SPC/E water for a polymer
> (hydrocarbon) in water system within ffG43a2 force field?
> Second part of my question:
> The Gromacs topology directory provides only spc216.gro file. Is the
> configuration file (to be used with genbox) same for both spc and spce?
> Is it enough just to use the "-water spce" flag in pdb2gmx to make sure
> I am using SPC/E water, while genbox uses the default spc216.gro?
> Regards,
> -- 
> Suman Chakrabarty
> -- 
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