[gmx-users] Conformational sampling

[nishap.patel at utoronto.ca]

Thanks. I am definitely going to look into that.


Quoting chris.neale at utoronto.ca:

> Nisha:
>
> Simply applying available tools and seeing if the distribution looks
> okay is not a good plan. You should have a very well-defined idea of
> what you are trying to test and then pick a tool to get that done.
>
> For example, perhaps you have a reference that provides the converged
> distribution of a dihedral and you want to see if your run reproduces
> this value. You would then use some tool, or combination of tools, to
> calculate the dihedral values and create a histogram of them.
>
> Without an outside standard, it is certainly impossible to use a
> single run to prove that your sampling has converged. It is only
> possible to prove that it either (a) remains unconverged, or (b) that
> there is no evidence that it is unconverged.
>
> In this case, if you really care about it, the best thing to do is to
> run a few separate simulations starting from different starting
> conformations (be sure to start from different dihedral basins). Then
> plot the time-average of some observables (e.g. the distribution of
> sampling of a given dihedral) and the values from different runs
> should "converge" to the same distribution if you run long enough --
> this is the true meaning of convergence, what many people do by way of
> things like block averaging is just a hack since one usually only has
> the resources to run a single trajectory.
>
> And don't forget that there are more things to converge than just
> dihedrals. You could also look at pairwise combinations of dihedrals,
> etc. Note that I'm trying to keep the advice general here because I
> assume that you're eventually going to tackle something more complex
> than glycine.
>
> Chris.
>
>> 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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