Amit Choubey wrote:
Thank you,
Is it really necessary for me to use Charmm FF for all atom calculations
on lipids?
You can use whatever model you want, provided it's valid. Just so happens that
most people who use all-atom models of lipids use CHARMM.
The reason I am asking this is because it will require me to create
gromacs compatible FF files of the Charmm FF . I did find two perl
scripts which can do probably handle that but i am wondering if the
compatible FF are already up on gromacs website somewhere.
No one ever said life was easy :) CHARMM support is under development, you can
get the source via the git repositories, but I don't know its current status.
-Justin
amit
2009/10/14 LuLanyuan <lulany...@msn.com <mailto:lulany...@msn.com>>
Hi,
You can find some configurations here:
http://persweb.wabash.edu/facstaff/fellers/
And I think you can use Charmm FF.
Lanyuan
------------------------------------------------------------------------
Date: Wed, 14 Oct 2009 11:29:26 -0700
From: kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Subject: [gmx-users] question about all atoms lipid molecule
structure and force field
Dear all,
I have been trying to search for an all atom DPPC sructure
(including the missing Hydrogens of long chain hydrocarbons) and
then do an all atoms md simulation on it. I havent yet found any
such structure or any force field that could be used for it on the
internet. Is anybody familiar with any such work ?
Is there any all atom model for hydrocarbons which is incorporated
in Gromacs? I am not 100 % sure about it.
I want to do this to parametrize another force field which
essentially uses all atom model.
Thank you,
Amit
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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