[gmx-users] starting conformation different
Mark.Abraham at anu.edu.au
Wed Dec 27 08:16:07 CET 2006
priya priya wrote:
> Dear All
> If i start MD with different geometries for the same peptide fragment,
> ie. different conformation (phi,psi angles)..........and run the
> simulations for 5ns on all the conformations.....i get different results
> from all the fragments simulated in vacuum.
This is a bit like baking bread either with egg or with no egg and
varying the amount of flour each time. The flour will cause minor
variation and the egg content will make for a result that does not
resemble the alternative...
> Please suggest me the criteria for selecting the appropriate structure
> from all the final conformations obtained.
Unfortunately that's your job, and it depends what you intended the
exercise to produce.
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