[gmx-users] REMD problem

Liu, Liang liu4gre at gmail.com
Fri Sep 30 01:57:52 CEST 2011

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

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

On Thu, Sep 29, 2011 at 4:24 PM, Mark Abraham <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, 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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Liang Liu
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