[gmx-users] Conformational sampling

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Mon Aug 9 23:11:05 CEST 2010


Well I guess, what I am trying to get at is, for my system I want to  
make sure that 100ns has covered all the conformational changes within  
the molecule, although I know there is not that much conformational  
changes for glycine molecule, but I just wanted to confirm. I did run  
g_angle command and I got the theta values for different groups and  
the distribution looks okay according to me (I compared the average  
angle values that I obtained from g_angle to the actual angle values.




Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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
>
> ========================================
> -- 
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