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From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Thu May 19 2011 - 04:15:26 CDT

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On Tuesday 17 May 2011 18:34:04 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.

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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