[gmx-users] Conformational sampling

[nishap.patel at utoronto.ca]

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.
>
> -Justin
>
>> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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