AMBER Archive (2008)

Subject: Re: AMBER: corrupted restart file

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Tue Jun 03 2008 - 05:13:29 CDT

Hi,

I guess the best way to deal with this is to , first, find out what snapshot your corrupted restart file corresponds to in your trajectory file. Then, extract the corresponding snapshot (in restart format) from the trajectory by ptraj. Fill in the missing coordinates in your corrupted restart file by comparing to the restart file you extracted from the trajectory. You may have to delete the last digit number to properly place the missing coordinates in your corrupted restart file.

Also, you may want to run longer iterations (nstlim=20000 to 50000 would be OK i guess, depending on how long you would like to run your MD) to diminish problems due to some coordinates dissipating way off of the range for MD experiments longer than 40 ns. Using 'IOUTFM=1' command in your input file (for netcdf binary trajectory format) may also help reduce the size of your trajectory by upto 60%.

Good luck.

jenk.

Cenk Andac, M.S., Ph.D. Candidate
 School of Pharmacy at
 Gazi University-Ankara Turkiye
    Address: Bandirma Sok. No:6
  Etiler, Ankara, 06330 Turkey
  Cell: +90-(536)-4813012
  E-Mail:cenk_andac_at_yahoo.com

--- On Tue, 6/3/08, yavuzturkm_at_prc.boun.edu.tr <yavuzturkm_at_prc.boun.edu.tr> wrote:

> From: yavuzturkm_at_prc.boun.edu.tr <yavuzturkm_at_prc.boun.edu.tr>
> Subject: AMBER: corrupted restart file
> To: amber_at_scripps.edu
> Date: Tuesday, June 3, 2008, 4:18 AM
> 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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