[gmx-users] Position restraint problem

[David]

On Wed, 2002-11-27 at 19:45, Arpita Aravind wrote:
> Hi,
> I am trying to perform MD simulation on my protein
> consisting of chains A (451 residues) and B (444
> residues) and neutralized by 46 NA+ ions. On
> performing "gmxcheck" on the the trajectory file
> obtained after the short MD with position restraint, I
> find that a large no. of heavy atoms like the carbon
> atoms are overlapping (i.e. the average distance
> between them is less than the sum of both Van der
> Waals radii). '
Are you sure? This would mean huge vanderwaals (LJ) energies. Could it
not be something with visualisation?


-- 
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://zorn.bmc.uu.se/~spoel
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