AMBER Archive (2004)

Subject: Re: AMBER: Question about restart MD

From: Carlos Simmerling (
Date: Mon Oct 11 2004 - 13:55:39 CDT

Xin Hu wrote:

> Dear Amber user,
> I was runing a 2ns MD simulations using Amber8. While the job crashed
> at about 1.5 ns (around NSTEP=750000), I restarted the job by using
> the restart coordinate file and giving a new file name for -r
> (md_new.rst) and -x (md_new.mdcrd). The job was restarted at about the
> 1.5ns (not the exact stop time) but the NSTEP started from the
> begining (NSTEP=100). THe problem is that the job was still running
> even the time up to 2.5 ns (because of the NSTEP). Should I change the
> "nstlim=1000000" before restarting the simulation or some other
> options I should change to control the restart time?

yes, you should usually change it to reflect the number of steps that
you want to run AFTER the restart. however, the results you have are
fine, so it
probably isn't worth changing anything.

> Is there any way to add the restart output (mdcrd,..) to existing
> files while not creating a new one (mdcrd) ?

not directly, but ptraj can combine the mdcrd files into 1 file when you
are finished.

> Another question, I mannually terminated the MD job and process the
> two trajectory files (initial + restart) using ptraj. When I plot the
> rms, I found there is a big change right at the time of 1.5 ns (from
> 1.2A remarkedly to 2.5A). Is it because of the restart (or restart
> unproperly)?

that seems like a problem, you might want to check your restart input
carefully. there
are many things that could be the problem, so I can't really help. maybe
you didn't use the
right input coordinates, maybe the restraints weren't right (if you used
any), maybe
the temperature or box wasn't right, etc. you should look carefully at
the sander output
at the end of the first run and the start of the second, they should be

> Thank you for your help.
> Xin
> ---

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