[gmx-users] Berger lipid

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Jun 30 19:25:24 CEST 2012 

Dear Peter,
I appreciate your explanation  :)  


Regards,

Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, June 30, 2012 8:57 PM
Subject: Re: [gmx-users] Berger lipid

323 is proper for a higher melting point lipid like DPPC. You can easily 
simulate POPC at 300, and many other people have done so.  In fact I received 
criticism from a reviewer as to why I picked an elevated temperature of 310, 
despite the fact that 310 is physiological temperature (to make some 
experimentalist reviewers happy). Some early rhodopsin runs were done at
310 and I'm pretty sure that was included as a reference in the rationale
for the elevated temperature (besides the standard "310 is well above the
solid phase transition temperature for POPC" line). Neither the g_membed
authors nor Klauda run POPC above 310K if I remember correctly.

On 2012-06-30 07:33:38AM -0700, 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 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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> -- 
> ==================================================================
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> pcl at uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
> ==================================================================

-- 
==================================================================
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
pcl at uab.edu            | Birmingham AL 35294-4461
(205) 690-0808            |
==================================================================

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