[gmx-users] problem with npt

Mark Abraham Mark.Abraham at anu.edu.au
Sun Dec 16 12:35:48 CET 2007

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.


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