[gmx-users] REMD problem

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 30 13:26:45 CEST 2011

Liu, Liang wrote:
> Thanks. Actually I applied just because the tutorial said so :(
> What I need is the structures only, I googled, but did not obtain useful 
> information about Gromacs with REMD. Maybe I need to read the manual 
> again :(

What structure(s)?  The .xtc files contain the coordinates along each trajectory 
(ensemble-continuous), and the final snapshot is written to a .gro file by mdrun 
(although these do not necessarily tell you anything by themselves).

> I am totally fresh to MD simulation, just worked on this for 1 week ...

Back up.  REMD can be very complex, especially if you want to do it right.  Do 
some basic tutorial material (standard MD) and understand the workflow and 
analysis.  Spend time in the literature, as Mark suggested.  The time investment 
you make now may delay your actual data collection by a few weeks, but will save 
you months of wasted time overall if you try to plow ahead without a clear 
vision for what you're doing.


> On Thu, Sep 29, 2011 at 4:24 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 30/09/2011 2:50 AM, Liu, Liang wrote:
>>     After running for more than 12 hours, the REMD simulation is
>>     completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files.
>     Yep. One for each simulation.
>>     Not sure if the result is reasonable.
>     Justin told you yesterday they would not be, because you have made a
>     number of totally arbitrary choices.
>>     I tried to analyze the result, and after applying demux.pl
>>     <http://demux.pl/>, two files replica_index.xvg  replica_temp.xvg
>>     are obtained.
>     Why did you want to demux?
>>     My question is how to obtain the structure information? (I will
>>     need pdb file).
>     Do all the tutorial material you can find - even if not strictly
>     relevant - to get an idea about good workflows. Then try to
>     replicate (part of) a published REMD study to see how things work
>     there. Search the web and check out the GROMACS web page - there's
>     lots of material out there. Stabbing in the dark is a great way to
>     waste your time, and people here don't have the time to teach every
>     person every thing.
>     Mark
>     --
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> Best,
> Liang Liu


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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