[gmx-users] Berger lipid

[Shima Arasteh]

Thanks Justin.
Yes, you are right. You wrote the tutorial for DPPC and I know that.

ok, I saw the temperatures upper than 271 K is proper for POPC. It's acceptable that 310 mentioned in Peter's paper is correct. But I'm wondering how they chose "310" K? In his article, he explains that their study was done in mammalian cells.

 
Sincerely,
Shima


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, June 30, 2012 7:15 PM
Subject: Re: [gmx-users] Berger lipid



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

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