[gmx-users] Conformational sampling

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> So is there a way I can test for convergence for my zwitterion for 100ns 
> run?
> 

I'm not yet clear what you're assessing or how you define convergence.  In 
addition to what Chris said, you can look at dihedral transitions with g_angle. 
  Surely there are a few dihedrals aside from standard phi/psi, but I don't know 
what that's going to tell you.

-Justin

> 
> 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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> 
> 
> 

-- 
========================================

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

========================================