[gmx-users] Conformational sampling

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Fri Aug 6 17:08:07 CEST 2010


     I would like to do conformational sampling for my simulation of  
one glycine in its zwitterionic form in water and obtain a PMF curve  
to see if the system is equilibrated and that all possible torsions  
are covered for my 100ns run. I am not sure how to approach this  
issue. Is there a tutorial I can follow? Do I need to do umbrella  
sampling and use WHAM to extract PMF?

I would appreciate some help!

Nisha P.

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