Dear Amber-users,
When I restart to run MD (pmemd) after 48 NS MD simulation using the restart file made at the step 48 NS from the previous cycle I got an error like below and job was immediately stop.
vlimit exceeded for step 427; vmax = 63.7283
vlimit exceeded for step 428; vmax = 20.4282
vlimit exceeded for step 429; vmax = 40.0177
vlimit exceeded for step 430; vmax = 20.4311
vlimit exceeded for step 431; vmax = 29.3222
vlimit exceeded for step 432; vmax = 33.9563
vlimit exceeded for step 433; vmax = 27.1015
vlimit exceeded for step 435; vmax = 20.8956
vlimit exceeded for step 437; vmax = 80.3997
Then I checked the RNA structure model generated at the step of 48 NS (nano-second) I found part of RNA was out of the box.
Also one strand of RNA was split from the RNA complex and was lying outside the box. As I know that
under periodic boundary conditions, when the restart file was read in MD simulation, the molecules will be re-translated into the central box before the first MD step.
I checked my input file for MD, I always used the iwrap=1 to control I/O. I also used the "ptraj" program to post-process my restart and trajectory files, however, the problem was not resolved.
I need your help. Thank you very much!
Regards,
Shu-Yun
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Received on Wed Jun 30 2010 - 14:00:03 PDT
