ram bio wrote:
Dear Justin.
Thanks for the suggestion, definitely i would run next time for a
longer time 2-10 ns.
Here, I want to learn the analysis part of the mdrun, In order to
locate the lowest energy frame I executed command g_energy -f
md_0_1.edr -o PE.xvg and the output was
Statistics over 500001 steps [ 0.0000 thru 1000.0001 ps ], 1 data sets
All averages are exact over 500001 steps
Energy Average RMSD Fluct. Drift Tot-Drift
-------------------------------------------------------------------------------
Potential -1.2189e+06 1115.54 1070.01 -1.0927 -1092.7
then I had a look at the PE.xvg file, but the values are very close to
identify the lowest energy point, i also tried to a have a look at the
md_0_1.log file, here also it is tedious and time consuming and the
values are close to remember. Can you suggest me how to locate the
lowest energy frame, so that i can use the comand (below) to retrieve
that particular frame coordinates in PDB file:
I would suggest writing a script. I think plotting tools like Grace can also
extract minimum values from data sets. If the values are so close together,
then ask yourself whether the lowest of these values is significantly different
from any of the other conformation. Also, an RMSD analysis will tell you how
much the structure has changed (or is changing).
trjconv -f md_0_1.xtc -o LEconf.pdb -dump framenumber (any frame
number- corresponding to the lowest energy)
and also please tell the whether the command i am going to use to
retrieve the lowest energy configuration is correct.
Close. You also need to use -s when interconverting formats (I believe), and
-dump is not given a frame number, but rather a time in ps.
Thanks,
Ram
On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
ram bio wrote:
Dear Justin,
Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, i want to collect the
structure (coordinates in pdb) representing average of all the
frames/configurations produced in MD and also the lowest energy
configuration structure (coordinates in PDB) produced during the
simulation, which can be used for docking. Please help how to obtain
the average structure as well as the lowest energy configuration
structure.
Average structures are not always meaningful (or even physically-relevant):
http://www.gromacs.org/Documentation/Terminology/Average_Structure
You can get average structures from, i.e. g_cluster -cl, if you want. As
for the lowest energy structure, analyze potential energy, and dump out the
frame corresponding to the lowest point. Hopefully you saved coordinates
and energies at the same interval :) The potential energy will correspond
to that of the system, but hopefully it should give some indication of the
lowest energy configuration. I don't know anything about your system, but
it will also depend on how much the energy fluctuates as to how relevant
this structure might be, and how different it might be from an "average."
If your structure comes from some model you built, realize that 1 ns is an
exceptionally short time frame, especially given the capabilities of modern
hardware and the speed of the GROMACS code. You may want to consider
running a bit longer to ensure that you really have a stable system.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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
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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