[gmx-users] Conformational sampling

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 9 22:52:27 CEST 2010

nishap.patel at utoronto.ca wrote:
> 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

For a zwitterion, these torsions don't exist.  To measure phi, you need at least 
C-N-CA-N, and for psi N-CA-C-N.  For a single zwitterion, you have only N-CA-C. 
  You need at least a dipeptide.


> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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