[gmx-users] Conformational sampling
nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Mon Aug 9 22:57:34 CEST 2010
So is there a way I can test for convergence for my zwitterion for 100ns run?
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 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
>> -Nisha P
>> Quoting chris.neale at utoronto.ca:
>>> 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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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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