AMBER Archive (2008)

Subject: Re: AMBER: corrupted restart file

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 03 2008 - 05:15:21 CDT

do you have iwrap=1? imaging will solve the problem.
start from the last good restart and rerun. if that loses
too much data, you could try using ptraj to convert the final frame
of the trajectory to a restart format (but you will lose precision
and also not have velocities).

check the archives for iwrap, there is lots of detailed discussion.

On Tue, Jun 3, 2008 at 5:18 AM, <yavuzturkm_at_prc.boun.edu.tr> wrote:
> Hi all,
>
> I am running md simulations using Amber 8 (pmemd). I have 56 ns of
> simulations without encontering any problems, I can not run the next
> step, because the restart file of the final step is corrupted. The file
> contains the following lines somewhere, in between the whole coordinates:
>
> line 10619 to 10625 of 39259 lines:
> -26.6616571 27.6196336-204.3938941 -25.6883973 26.6103212-204.9640159
> ************-581.6656240 51.2153856************-581.7093637 52.0103458
> ************-582.3228373 50.6345810 83.3564486 141.1033530 374.3139541
> 83.2847264 141.0176154 373.3633034 83.7825960 140.2939694 374.5959620
> 123.5404905-133.4723244 142.4061610 123.3115033-134.3643324 142.1451661
> 122.9869954-132.9135814 141.8605593-324.2469570 386.7989805 224.7005756
> -323.3939942 387.2004493 224.8664344-324.2258923 386.5667011 223.7722252
>
>
> I believe the problem is related to the digit limitations encountered
> while writing the file. How can I solve this problem? The coordinates file
> does not contain such coordinates. I have already re-run the final step in
> case, but the same problem occurs. Can I generate the restart file from
> the coordinates of the final step?
>
> Thanks
> Melda Tozluoglu
>
>
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