From the link J B gave, they run 400/500 ns for each lipids, it seems
to be good. probably we can just read the paper J B mentioned to see how
it well for protein/membrane system.
Albert
On 06/22/2012 07:45 AM, Vlad Cojocaru wrote:
> 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 - 23:00:04 PDT
