Re: AMBER: Restart Files

From: Carlos Simmerling <>
Date: Fri, 2 Mar 2007 10:32:46 -0500

yes you should read velocities. ntx=5 and irest=1 are fine for GB.
It seems like there is a problem with the file reading- check your stderr
file to see the error message (perhaps in the queue error output,
it depends on how you are running the sander job).
Also you can use a file editor to look at the restart file
and make sure it is ok, the file format is given on the amber web site.

does the same job work with ntx=1 and irest=0? are you sure the restart
file has velocities? (restart files from minimization do not)

On 3/2/07, Steve Seibold <> wrote:
> Hello Amber
> Sorry, but I am afraid I have what is probably a simple question. I have
> been running gb simulations (MD) with NTX=1 and IREST=0 and out putting
> restart files. However, I thought I should be running using the restart
> file's velocities of the former run to extend my production runs (MD). Thus,
> I set NTX=5 and IREST=1. When I did this my simulation freezes at the point
> "ATOMIC COORDINATES AND VELOCITIES" shown in the output file. It is as if it
> is stuck searching for the velocity inputs. Can I use NTX=5 and IREST=1 for
> implicit solvent? I know that I do not have box information; is that the
> problem?
> Any advice/explanation would be greatly appreciated. I tried reading
> through the manual and search the AMBER web site, but could not locate
> anything that explicitly addressed this.
> Cheers, Steve

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Received on Sun Mar 04 2007 - 06:07:54 PST
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