[gmx-users] REMD problem
Mark.Abraham at anu.edu.au
Fri Sep 30 01:24:15 CEST 2011
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
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.
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