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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