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.
-Justin
Sincerely,
Yao
--- On Wed, 10/6/10, Berk Hess <g...@hotmail.com> wrote:
From: Berk Hess <g...@hotmail.com> Subject: RE: [gmx-users] charmm tip5p in
Gmx 4.5.2 To: "Discussion list for GROMACS users" <gmx-users@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.p...@cbr.su.se To: gmx-users@gromacs.org
Hi,
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?
Berk
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@gromacs.org
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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