When you use ptraj to post-process the restart files, all of the velocities
are discarded (and set to 0). You need to re-heat after you do this.
Good luck!
Jason
On Wed, Jun 30, 2010 at 4:58 PM, Le, Shu-Yun (NIH/NCI) [E] <
Shu-Yun.Le.nih.gov> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 30 2010 - 17:00:03 PDT
