[gmx-users] Conformational sampling

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Aug 6 18:24:15 CEST 2010


The approach is dictated by the goal. What do you want from this? and  
why are you doing it? e.g. if you want to test the FF, then it is a  
good idea to at least include US as a part of your strategy; if you  
want to determine if 100 ns of equilibrium sampling is sufficient to  
converge all torsions, then obviously you should not be doing US. In  
any event, would start by running some equilbrium simulations and  
analyzing the torsions with g_rama, g_chi, g_dih, etc. Be sure to read  
through the -h output of each program as there are some nuances.


-- original message --


      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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