[gmx-users] shell again

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 30 02:06:10 CET 2002

On Wed, 2002-10-30 at 15:03, Dmitry Kovalsky wrote:
> Hi there, 
> Tracing back a problem with option -shell ( Vol 1 #412) in genbox programm
> I have found out that depending on the shell value I get different results.
> I have used tried 0.3. and 0.15 nm shell and got very quickly (1 ns) two 
> distinct resulted conformations. 
> So I'm wondering how shell can influence the dynamics of a protein
just look at the screen. If you have too little water it will desolvate
most/part of the protein, leaving you with a vacuum simulation. People
using shells of water usually simulate a limited time, or with many
restraints. There are also potentials (but not in gromacs) that take
care that no water evaporates, or gets ordered on the surface. Check out
work by the Aqvist group.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 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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