[gmx-users] shell again
dikov at imbg.org.ua
Mon Nov 4 13:45:04 CET 2002
On Monday 04 November 2002 13:00, gmx-users-request at gromacs.org wrote:
> So, you create a 'free space' in between the protein and your water?
> Why whould you want that?
As I can understand it is a trick frequently used in MD in order to get faster
equilibration of system. (Or I'm wrong?)
If I use the 'free space' the pressure in system does not jump to 200 or so.
The case is in width of shell if I use 0.15 it is stable (beacuse only 15
moleculaes was removed) if I use 0.3 -- not. Is there any princliples of
using it ?
Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
E-mail: dikov at imbg.org.ua
Fax: +380 (44) 266-0759
Tel.: +380 (44) 266-5589
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