yes, absolutely
now, I am not sure what you mean by 'not usable'
if you mean that data is missing or corrupted, then either the file was
not fully written when you hit the wallclock
or that your molecular is flying outside your box (if you see *** for
instance).
Now, can you visualize the restart file into vmd ?
if that does not work, then the file is truncated/corrupted.
If you can visualize it, try running a regular sander/pmemd run without
smd. If that works, then the restart is fine...
Remember that to restart an SMD run you MUST change the restraint file,
since you are now starting your SMD from whatever coordinates you last
saved !
Adrian
On 10/12/11 4:39 PM, Mo Chen wrote:
> Hi Adrian,
> I understand that. I actually meant to say that I heard the restart file of
> SMD simulation is not quite usable even if my simulation did not run out of
> the wall time. Basically I have just heard that, but I am sorry I have not
> tried myself and I did not know why. In your last email, do you mean if the
> restart file is saved properly before the end of the walltime, I should be
> able to use it as a restart file? Thank you very much!
>
> Best,
> Mo
>
> On Wed, Oct 12, 2011 at 4:30 PM, Adrian Roitberg<roitberg.qtp.ufl.edu>wrote:
>
>> This has nothing to do with SMD runs.
>>
>> If you hit the wallclock time, you sometimes do not see the 'last'
>> restart fully written.
>>
>>
>> You can pick the last frame form the mdcrd and create your new restart.
>>
>> Adrian
>>
>>
>> On 10/12/11 4:26 PM, Mo Chen wrote:
>>> Dear Amber users/developers,
>>> I am trying to run SMD simulations on Ranger, but my simulations could
>> not
>>> finish before the maximum runtime (24 hours) even though I would use the
>>> optimal number of cores. And I heard the SMD restart file is not quite
>>> usable, but I did not understand why. May I ask anyone has encountered
>>> similar situations? And how should I solve this problem? Thank you very
>>> much!
>>>
>>>
>>> Best,
>>> Mo Chen
>>> Graduate Student
>>> 120 Stocking Hall
>>> Cornell University
>>> Ithaca, NY 14850
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> --
>> Dr. Adrian E. Roitberg
>> Professor
>> Quantum Theory Project, Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Wed Oct 12 2011 - 14:00:04 PDT
