[gmx-users] Berger lipid

[Justin A. Lemkul]

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 <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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-- 
========================================

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

========================================