Re: hi

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Thu May 19 2011 - 04:29:14 CDT

On Wednesday 18 May 2011 10:43:25 kanchi subbarao rao wrote:
> hi all
> i am new namd user. i am running simulation of dppc-bilayer by using
> charm-27 force field. i am facing a problem how to maintain constant area
> per lipid while running simulation in NPT and NVT ensembles.
>
>
>
> thanking you
> subbarao kanchi.

Why are you crossposting to VMD-List?

Well, I'll cite miyself ;-)

If your setup is new, and you don't have to stick with C27 FF you should
switch to C36 FF (It is freely available from MacKerells Website
http://mackerell.umaryland.edu/CHARMM_ff_params.html). With this FF you should
obtain the correct area/lipid.
Read:
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on
Six Lipid Types "J. Phys. Chem. B, 2010, 114 (23), pp 7830–7843"

Otherwise use an NPgT (g = gamma) or NPaT (a = area) ensemble.
Tweak "g" or "a" so that you match e.g order parameters obtained from
literature or NMR experiments. Remember to equilibrate long enough to get some
reasonable ensemble averages.

Cheers,
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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