[gmx-users] Conformational sampling

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> 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.
> 
> 

Then that's probably the best you can do for a molecule as simple as glycine.  I 
would certainly think that rotation about such few bonds would happen within 
even less time than 100 ns.

-Justin

> 
> 
> 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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> 
> 
> 
> 

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

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

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