AMBER: Question about restart MD

From: Xin Hu <>
Date: Mon, 11 Oct 2004 14:38:38 -0400

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.


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Received on Mon Oct 11 2004 - 19:53:00 PDT
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