[AMBER] Fwd: Replica exchange problem in visualization and interpretation of the MD out files

From: maryam azimzadehirani <maryamai1988.gmail.com>
Date: Fri, 27 Nov 2015 18:58:09 +0800

Dear Amber users,
I have been trying to do REMD simulation on a 50 a.a peptide following the
A7 Amber tutorial. I am not new to MD simulations but I have been
struggling about some issues.
*First* is now I ran the replicas just as long as the tutorial (500 steps),
how do I know what is the proper length of replicas for my own system? Is
there anyway to calculate? paper? methodology? etc.
*Second* is the md.out files of my replicas, some of my exchanges were
successful and some were failed.As there are no more explanation in the
tutorial, I have problem interpreting the output files. I attached two
examples(failed and successful one here).
*Third* is I have problem visualizing the remed trj files. Just to simply
visualize the system I tried grep -v REMD but couldn’t load it in VMD. I ll
attach the original sander out trajectory and topology file here ( I have
removed it, so that my mail could be posted, will send it back if
Will be very grateful if you could help me with these issues.
Best Regards,

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Received on Fri Nov 27 2015 - 03:00:03 PST
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