Re: [AMBER] R: strange POPC under lipids 11 FF

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Fri, 22 Jun 2012 07:45:01 +0200

I saw these on a poster at a recent conference. I did not read the paper but from the poster I understood that they are very much based on charmm36. Unfortunately I could not speak with the author.

I would like to say that people should be cautious when deciding if 2 force fields are cmpatible. A qualitative agreement is not enough. A quatitative reproduction of experinentally derived energies is required.

All I want to say is that those who would like to use these parameters for protein-membrane (with amber proteins) simulations should carefully assess the combatibility issue before running massess of simulations.

Vlad

---
Dr. Vlad Cojocaru
Max Planck Institute Muenster
Roentgenstrasse 20,
48149 Muenster, Germany
Tel: +49-251-70365324
Sent from my mobile phone; Sorry for being short and for any errors
J B <john.b.86.hotmail.com> wrote:
I am a Gromacs user and I have tried these parameters that are supposed to be compatible with the AMBER force fields:
http://web.me.com/jambeck/lipids/Downloads.html
And they work well for saturated PC lipids without applying a surface tension and apparently parameters for unsaturated lipids are on the way.
Used a real space cut off of 10 angstrom and a LJ cut off of 12 Angstrom and got good results compared to experiments.
I guess that these parameters are easy to use in AMBER... 		 	 		 
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Received on Thu Jun 21 2012 - 23:00:03 PDT