On 6/30/12 10:33 AM, Shima Arasteh wrote:
Dear Peter, Thanks for your link and the article. I'd like to know more about
your paper. You've mentioned in it that the temperature of POPC equilibrated,
is 310 K. As I saw in Justin's tutorial , 323 K is proper, however it was a
I'll let Peter address the question directed to him, but I want to refute
something stated here. One should not say that for membrane simulations "323 K
is proper." I explain in the tutorial why this particular temperature is used
in the context of DPPC only. I also provide a table of phase transition
temperatures for several lipids to explain the reason why the elevated
temperature was required in this case.
-Justin
different system simulated and also many parameters are not the same as your
system . Would you telling me about the reason of 310 K?
Thanks in advance
Sincerely, Shima
----- Original Message ----- From: Peter C. Lai <p...@uab.edu> To: Shima
Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org> Cc: Sent: Friday, June 29, 2012 2:54 PM Subject: Re:
[gmx-users] Berger lipid
yes
http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract
The files are here: http://uab.hyperfine.info/~pcl/files/popc36/
On 2012-06-28 09:58:26PM -0700, Shima Arasteh wrote:
Yes, I remember now...................you are right :) But I didn't know
the linked you sent me, was your own output! However I wanted to know if
it is necessary to produce the .itp file on my own or not.
I still have this link, so will cite to you. It would be a good idea to see
its package in lipidbook too. Thanks Peter
Sincerely, Shima
________________________________ From: Peter Lai <p...@uab.edu> To:
Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Friday,
June 29, 2012 7:14 AM Subject: RE: [gmx-users] Berger lipid
Uh didn't we go through all of this like more than a month ago? I published
a paper using C36 POPC and even a linked to my popc.itp for it on this
list...
Of course Shima is welcome to pdb2gmx his own POPC, which I am fairly
certain will result in an identical file...
Lipidbook seems to only have C36 POPE. I guess maybe I will upload ours.
________________________________________ From:
gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of
Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, June 28, 2012 7:56 PM
To: Discussion list for GROMACS users Subject: Re: [gmx-users] Berger
lipid
On 6/28/12 8:54 PM, Shima Arasteh wrote:
Yes, I know that as studied the Kalp15 tutorial. Sorry, the last question
:) :
DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it
ok? Because I see that POPC.itp is also required for simulation of
protein in bilayer.
You need a topology of some sort. It depends on what parameters you have
on hand. If you do not have popc.itp from anywhere, then you need to
generate it somehow. If it is present in the .rtp file for CHARMM36 that
you have, then you can run pdb2gmx on it.
-Justin
-- ========================================
Justin A. Lemkul, Ph.D. Research Scientist 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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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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