[gmx-users] POPC Bilayer box

David spoel at xray.bmc.uu.se
Mon Apr 12 08:38:01 CEST 2004

On Mon, 2004-04-12 at 08:21, Simon Wang wrote:
> Dear gmx-users,
> I started from Peter's popc128a.pdb and extended the z dimension and readded 
> water. The system was stable in 200ps w/ PME. Then I scale the box size to a 
> larger one by genconf. The new system was fully minimized and run 50ps w/ 
> pr. on the lipid. During the simulation, however, the waters at the corner 
> of the box began to move to the middle and the density was incorrect. Please 
> enlighten me the reason for this and the possible solutions.
more details please, what did you do with genconf?

> Thanks in advance,
> Simon
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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