[gmx-users] GROMOS with SPC/E water?
suman at sscu.iisc.ernet.in
Fri Nov 14 20:14:58 CET 2008
On Thu, Nov 13, 2008 at 8:50 PM, Berk Hess <gmx3 at hotmail.com> wrote:
> 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:
Thanks for your response Berk. I shall try to cite that paper to
justify our use of SPC/E water. :)
> For configuration (gro) file, it does not matter much which starting
> 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?
>> Suman Chakrabarty
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