[gmx-users] shell again

[David van der Spoel]

> 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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