[gmx-users] shell again

Dmitry Kovalsky dikov at imbg.org.ua
Thu Oct 31 11:15:08 CET 2002

On Wednesday 30 October 2002 21:46, gmx-users-request at gromacs.org 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.

The problem is that I have near 11000 water mol in the system and distance 
from protein to box border is 1 nm. I don't think that effect of explicit 
solvent was disturbed somehow.

If I use 0.15 nm, resulted 1_ns_trajectory corresponds to NMR data in pico- 
and short nanosecond timescale, but if I use 0.3 nm the 1_ns_trajectory 
corresponds to possible timescale conformational changes that should be in 
middle nanosecond time scale.  

My suggestion is that in case of 0.15 water shell removal (16 waters) the 
system remain more tight (and may be more viscous) than in case of 0.3 (410 
waters) . Taking into account that it is quite little with respect to overall 
amount of water molecules the difference could only infuence the speed of 
conformational transition. It is like picture puzzle where to order 15 
numbers with one vacant place. In case of 0.15 there is 1 vacant place in 
caseo fo 0.3 there are two. If one needs to move number 1 to a proper place 
he should make 7 steps in the second case -- only 3. 

Am I right?

Sincerely yours,


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

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

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