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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