AMBER Archive (2004)

Subject: AMBER: Question about restart MD

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Mon Oct 11 2004 - 13:38:38 CDT

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 

---

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu