[gmx-users] energy analysis

[David]

On Sat, 2005-11-12 at 14:12 +0800, Wang Zhun wrote:
> Hi,
> 
> I performed MD simulation of  a peptide(in extended conformation) in vaccum for 2 ns, and used the
> resulted coiled conformation as initial structure for another 8 ns MD with same
> parameters. After energy analysis, I found the initial energy of the second 8ns
> MD was almost the same as the initial energy of the first 2 ns MD(about 400 kj/mol), instead of
> the final energy of 2 ns MD(-110kj/mol).
> Could someone explain this?
Please be more specific. Did you generate new velocities?
> 
> Thanks!
> 
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-- 
David.
________________________________________________________________________
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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