[gmx-users] Conformational sampling

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Mon Aug 9 22:48:17 CEST 2010

Okay so I tried to analyze the torsion using g_chi and g_rama for one  
glycine zwitterion in water. for g_rama I didn't see anything in  
xmgrace, and same for g_chi. I used this command for g_chi

g_chi -f traj.xtc -s gly.gro -phi -psi

When I run the command it says 1 residue with dihedrals found , 2  
dihedrals found. But when I open the log file its empty and so are the  
histo-phi/psiGLY.xvg plots. I tried using g_dih but it says:

Found 0 phi-psi combinations

I am not sure how to check for all torsion convergence for my glycine  
zwitterion molecule. Am I missing something in the command line?

-Nisha P

Quoting chris.neale at utoronto.ca:

> Nisha,
> 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.
> Chris.
> -- original message --
> Hello,
>       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!
> Thanks.
> Nisha P.
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