[gmx-users] shell again

[Dmitry Kovalsky]

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 ?


Sincerely yours,

Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143
UKRAINE

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589