[gmx-users] (no subject)

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 23 12:15:02 CEST 2004

On Thu, 2004-09-23 at 11:53, Robert d'Rozario wrote:
> Hi,
> I was wondering if anyone has this same problem, its a bit worrying.
> I am simualting an alpha helix in DMSO with PME.  I have 3 separate
> trajectories, each a continuation.  The first one runs from 0-4ns then
> 2nd one 4-6ns then the 3rd 6-10ns.  I have then concatenated the files
> which runs from 0-10ns.  At 6.1 ns I viewed the system, using VMD, and it
> seems to freeze as if the positon restraints are on everything.
> Any help would be greatfully appreciated
start by checking energy terms, temperature,pressure. Then compute a
mean square displacement for your molecule.
> Robert D'Rozario
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 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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