RE: AMBER: Restart Files

From: Steve Seibold <>
Date: Fri, 2 Mar 2007 14:52:39 -0500

Hi Gustavo
I am sending you my output file to show you were it pauses for an
extended period of time (~ 20 minutes). It has now started printing the
"Results" to the output file.

Thanks, Steve

-----Original Message-----
From: [] On Behalf
Of Gustavo Seabra
Sent: Friday, March 02, 2007 1:06 PM
Subject: Re: AMBER: Restart Files

Hi Steve,

My first thought is that you could have a large ntpr, so that it is
taking longer to reach the point to print anything. However, the
simulation should *not* get stuck at the "3" part. You should at least
see the header for the "4. RESULTS" part. Can you give us more details,
maybe some input fiiles?


Steve Seibold wrote:
> Carlos
> 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
> *To:*
> *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
> does the same job work with ntx=1 and irest=0? are you sure the
> 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 - 06:07:59 PST
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