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" <jalem...@vt.edu>:
nishap.pa...@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" <jalem...@vt.edu>:
nishap.pa...@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.ne...@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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