Dear developers,
I am writing you because I just installed the new version of Amber (Amber12). After the installation I
performed the analysis test for all the tools available in amber, and everything went fine. Thus, I tried
to run a SMD job (of about 20ns), using the pmemd.MPI protocol. Also in this case everything went
fine, the only problem is a sort of delay of Amber (a sort of lag time) in writing the text file containing
the distance, the force and the work done during the simulations (this file is usually called dist_vs_t).
My concern refers about the fact that I am working on a public CPUs workstation cluster (a University
Consortium), where I have a limited number of hours for the queues and for the job (usually 72
hours), so when the time useful for the calculation was expired I obtained the exact number of frame
for the SMD run (i.e 2000 frames), but a reduced number of values in the dist_vs_t file (i.e 1500). I
think that this is due to the delay of Amber in writing the file text for the dist_vs_t file.
I would ask you if exist a way to reduce the lag time with which amber write the dist_vs_t data, so as
to have the same number of frame and dist_vs_t values at the end of the calculation (when the
simulation is stopped, because of the expiration of the queues hour on the public workstation).
Thank you very much for your collaboration
Kindest regards,
Agostino
--
Agostino Bruno, PhD
Dipartimento Farmceutico
Universita' degli Studi di Parma
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Received on Thu Jul 26 2012 - 03:30:03 PDT
