[gmx-users] problem with npt

Eric Jakobsson jake at ncsa.uiuc.edu
Mon Dec 17 01:46:34 CET 2007

In our experience the leaflets of a bilayer have a tendency to 
separate if the cutoff on the van der Waals force is too short.  We 
always use 18-20 angstroms for that.

At 05:35 AM 12/16/2007, you 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.
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896  Fax 217 244 9757

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