Re: [AMBER] To continue the job-Reg.......

From: Mark Williamson <>
Date: Tue, 23 Nov 2010 13:17:28 +0000

On 23/11/2010 06:18, parasu raman wrote:
> Dear Amber groups,
> I am using Amber9 software to create the topology and coordinate
> file for 10ns Molecular Dynamics Simulation and the job was running on NAMD
> platforms. And the NAMD command line is
> Username/namd/NAMD/namd2 complex.inp>complex.out&
> Unfortunately the job was stopped at 7.9ns due to the external
> disturbance, kindly suggest me to, How to continue the job from the previous
> ns (from 7.9ns) and which is the exact command for the same?

Dear Parasu,

You are asking how to restart a molecular dynamics simulation and to do
this one needs the last set of coordinates and associated velocities.

However, you are using the NAMD molecular dynamics engine which is not
actually written by the AMBER developers who reside on this list. Hence
they will probably not be able to help you with a restart protocol since
this will be specific to the molecular dynamics engine i.e. NAMD, with
which the simulation has been run.

I would suggest either reading the NAMD user's guide at:

or posing this question on NAMD's mailing list:


Mark Williamson

AMBER mailing list
Received on Tue Nov 23 2010 - 05:30:03 PST
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