[gmx-users] shell again

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 31 00:10:18 CET 2002

> 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?
What do you mean with shell removal?
Do you use the protein in a shell of water in vacuum, or do you add the
whole box to it as well?

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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