RE: AMBER: Restart Files

From: Steve Seibold <>
Date: Fri, 2 Mar 2007 12:01:19 -0500


Thanks for your response. I checked the restart file and it does have
the velocities. I am beginning to think that it is not an AMBER problem,
but a computer problem. I "think" that what is happening is that the job
is running even though my output file is not being written to. That is,
my output file shows data up to "3. ATOMIC COORDINATES AND VELOCITIES"
and it has stalled there now for about 20 minutes. However, when I look
at the node processors they are running and the queue error file
contains no information accept what processors I am running on. So, I am
just going to wait awhile and see if it, over time, prints out to the
output file. My suspicion is that it will. It is just taking much longer
on this computer cluster than on my runs on another computer system.

Thanks again for your help.


Thanks, Steve



From: [] On Behalf
Of Carlos Simmerling
Sent: Friday, March 02, 2007 10:33 AM
Subject: Re: AMBER: Restart Files


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
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 - 06:07:56 PST
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