[gmx-users] charmm tip5p in Gmx 4.5.X
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 6 21:32:34 CEST 2010
Yao Yao wrote:
> Hi Berk,
> Thanks for your reply.
> Actually I followed the fws-peptide simulation in Dr. JE Kerrigan's tutorial,
> but in charmm27 force field with tip5p water.
> Before several warnings in the simulation step, I found that even in energy
> minimization step the protein cannot be settled. I sent my mdp file to the
> forum, and got an ok from Justin.
> So I am concerned about the compatibility between tip5p and charmm force
> field in gromacs, as well as the potential improvement in the new version.
What improvement do you believe to exist? The latest revision involving TIP5P
and CHARMM (on September 10) was to remove TIP5P from the list of possible water
models in charmm27.ff/watermodels.dat so that users wouldn't combine CHARMM +
TIP5P. The suggested water model for CHARMM is TIP3P.
> --- On Wed, 10/6/10, Berk Hess <gmx3 at hotmail.com> wrote:
>> From: Berk Hess <gmx3 at hotmail.com> Subject: RE: [gmx-users] charmm tip5p in
>> Gmx 4.5.2 To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Date: Wednesday, October 6, 2010, 10:02 AM
>>> Date: Wed, 6 Oct 2010 11:53:56 +0200 Subject: Re: [gmx-users] charmm
>>> tip5p in Gmx 4.5.2 From: szilard.pall at cbr.su.se To: gmx-users at gromacs.org
>>>> Does anyone have an idea about what time the Gmx
>> 4.5.2 will be released?
>>> Soon, if everything goes well in a matter of days.
>>>> And in 4.5.2, would the modified tip5p.itp in
>> charmm27 force field be the same as that in current git version? What is
>> your motivation behind this question? Do you think there is something wrong
>> wit the current tip5p.itp?
>>> The git branch release-4-5-patches is the branch you
>> want to look at.
>>> Whatever is in there will be in the release (unless it
>> get removed :).
>>> -- Szilárd -- gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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