[gmx-users] Berger lipid

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jun 29 02:43:23 CEST 2012

Yes, I have studied the article by Jeffery B. Klauda and other articles related to C36. And know where the parameters of CHARMM36 were derived. 

By the way, when I search the lipidbook to find the .itp file I can't find it! What about the lipid .itp ? Is it required yet? ( in your tutorial it's written "lipid.itp - Berger lipid parameters" )


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, June 29, 2012 4:58 AM
Subject: Re: [gmx-users] Berger lipid

On 6/28/12 8:23 PM, Shima Arasteh wrote:
> Thanks.
> Yes, you told me this before CHARMM36 is better than CHARMM27. But I'm afraid of using  C36. Because I think it's a newer FF and and less studies have done by it. Then if I face a problem, I can't find a way through articles!
> Don't you think so?

CHARMM36 was developed by the core CHARMM developers and I have no reason to doubt it.  If there was ever a group to develop good CHARMM parameters, it's them :)

Simply being "newer" is not a reason to doubt it.  Have you read the paper where the parameters were derived?  The reproduction of experimental observables is quite good.  Ultimately, the choice is yours, but be ready to justify that choice to a skeptical audience (reviewers).


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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