[gmx-users] Protein Solvent Dynamics - Coordinates for docking

[Justin A. Lemkul]

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 <jalemkul at 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

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