[gmx-users] problem with npt

Andrei Neamtu neamtuandrei at gmail.com
Mon Dec 17 10:27:01 CET 2007

have you checked if there is no water inside the membrane after the
use of genbox?

On Dec 16, 2007 1:35 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> pragya chohan wrote:
> >
> > i started with the lipid coordinates from peter tieleman and removed the
> > water. then i added water by genbox.
> > I did energy minimization followed by position restrain, which I removed
> > gradually. all of it was done under npt. I carried out npt for 250
> > ps. During the next 250 ps npt run the bilayers separated and deformed.
> Usually NVT to get the temperature right before relaxing to NPT to let
> the density equilibrate can be good idea. Look at how much your box
> changed size during your NPT to see if this effect is causing problems.
> Mark
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