[gmx-users] Berger lipid

[Shima Arasteh]

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 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 <pcl at uab.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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 <pcl at uab.edu>
> To: Discussion list for GROMACS users <gmx-users at 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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at 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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