RE: deformations in a water box during equilibration in NAMD

Date: Fri Nov 03 2006 - 04:28:01 CST

Anybody knows how works the solvate module in VMD (used for NAMD)?
When I do

pakage require solvate
solvate protein.psf protein.pdb -t 5 -o outputname

is the programm creating boxes of water molecules miminized and
equilibrated or only molecules of water dispersed?

If I use the solvated protein created from this module for a
minimization and subsequent equilibration in NAMD, the water box is
deformed during equilibration. If the boxes of water are not
equilibrated, I suppose this could be the reason??

Thanks a lot in advanced.

Best wishes,

Rebeca García
Post-doctoral researcher
Universidad de Barcelona

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