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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