Re: AMBER: Question about restart MD

From: <>
Date: Mon, 11 Oct 2004 15:05:04 -0400

1. You should modify the "nstlim" variable before you restart the MD
run, so that the total nsteps of in the two run is what you want.

2. As far as I know, you can not add the output to the existing files.
But it's not difficult to merge the two crd files, isn't it?

3. It's possible to have significant RMSD jump during the MD run. But
you should make sure your velocity information is used for your
continuing MD run (check the irest value).


On Mon, Oct 11, 2004 at 02:38:38PM -0400, 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?
> Is there any way to add the restart output (mdcrd,..) to existing files while not creating a new one (mdcrd) ?
> 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)?
> Thank you for your help.
> Xin
> ---

I have no words to say.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Oct 11 2004 - 20:53:01 PDT
Custom Search