[gmx-users] Position restraint problem

David spoel at xray.bmc.uu.se
Wed Nov 27 21:28:47 CET 2002

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

More information about the gromacs.org_gmx-users mailing list