[gmx-users] REMD problem

Mark Abraham 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 
> 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.

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