AMBER Archive (2008)

Subject: AMBER: corrupted restart file

From: yavuzturkm_at_prc.boun.edu.tr
Date: Tue Jun 03 2008 - 04:18:25 CDT

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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