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

From: Carlos Simmerling <>
Date: Fri, 27 Nov 2015 09:35:12 -0500

a 50 amino acid peptide is still very challenging to do by MD and may
require microseconds of simulation. For examples of REMD input files and
analysis for systems this size, see
%A H. Nguyen
%A J. Maier
%A H. Huang
%A V. Perrone
%A C. Simmerling
%T Folding Simulations for Proteins with Diverse Topologies Are Accessible
Days with a Physics-Based Force Field and Implicit Solvent
%J J. Am. Chem. Soc.
%V 136
%P 13959-13962
%D 2014

On Fri, Nov 27, 2015 at 5:58 AM, maryam azimzadehirani <> wrote:

> 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
> necessary)
> Will be very grateful if you could help me with these issues.
> Best Regards,
> Maryam
> .
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Received on Fri Nov 27 2015 - 07:00:03 PST
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