Thanks. I am definitely going to look into that.
Quoting chris.ne...@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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