Hello,
I believe that pmemd does not update the mdinfo file as often as it updates
the mdout file due to performance implications. You can figure out the
source of this discrepancy by digging through the pmemd code, but this has
no effect on your results.
Hope this helps,
Jason
On Tue, Aug 17, 2010 at 11:10 AM, Mayank Daga <mdaga.vt.edu> wrote:
> Hi,
>
> I am a newbie using AMBER on the GPUs.
> When I run my simulations, I see two output files, mdout and mdinfo. In the
> mdinfo file, I see the timing details as to how many ns/day I get. The
> issue
> is some steps are always uncompleted according to this file while mdout
> lists that all the steps have been completed. Why is this discrepancy?
> For example, if I run a simulation for 10000 steps, mdinfo shows 9000 steps
> remaining while mdout list energy values for all 10000 steps.
>
> I am using the input files as downloaded from the AMBER website and to run
> the simulation:
> ~/amber11/bin/pmemd.cuda -O -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> -x mdcrd -gpu 0
>
> Please explain this behaviour.
>
> Thanks,
> ~mayank
>
>
> --
> Mayank Daga | SyNeRGy Laboratory | Dept. of Computer Science
> Virginia Tech | http://synergy.cs.vt.edu | http://www.cs.vt.edu
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 17 2010 - 09:00:03 PDT
