great - so adding iwrap=1 will solve it for future simulation as I
understand(?) but for long simulations you will have to image center
once in a while?
On Fri, Oct 21, 2011 at 3:37 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Oct 21, 2011 at 8:33 AM, <steinbrt.rci.rutgers.edu> wrote:
>
>> Hi,
>>
>> > I try to restart my simulation - I have been able to continue the
>> > simulation by restarting every 20 ns but after 80 ns I get a restart
>> > file which gives me the following error when I try to run it again
>>
>> do your restart files contain ******* entries? In long simulations, this
>> can happen if center of mass motion is not removed. The simulation still
>> finishes normally and a rst file gets written, since internally, the
>> coordinates are floats, but the fixed width format in the rst cant contain
>> the numbers anymore.
>>
>
> This is especially common in explicit solvent simulations if you don't use
> iwrap=1 (see previous posts on this list for more information). Even if you
> remove COM motion (via nscm), your solvent naturally diffuses, and will
> expand beyond the bounds of a fixed format restart file in terms of the size
> of coordinates that can be expressed.
>
> This should be fixed in the next release with the use of NetCDF restart
> files.
>
>
>>
>> If that is the case, image your last good rst file and continue from
>> there...
>>
>
> One thing you'll want to be careful of when you do this is to copy your
> velocities over after you've done this, since ptraj (and cpptraj in
> AmberTools 1.5, AFAIK) doesn't preserve these values, even if they exist.
>
> HTH,
> Jason
>
>
>> Thomas
>>
>> Dr. Thomas Steinbrecher
>> formerly at the
>> BioMaps Institute
>> Rutgers University
>> 610 Taylor Rd.
>> Piscataway, NJ 08854
>>
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Fri Oct 21 2011 - 07:00:04 PDT
