[gmx-users] starting conformation different

Mark Abraham 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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