Hello,
For the minimization step, is it possible to shorten the length of the simulation by decreasing the values for
maxcyc and nstlim? We are new to Amber and to MD and are therefore not entirely sure about the effects of the various parameters on the simulation. Initially, we were using sander.MPI because this is the version of sander that was used in the example minimization step provided in tutorial 3. Also, I just found out that pmemd has not been compiled on our cluster. Thanks a bunch,
Dan
On May 26, 2011, at 12:31 PM, David A. Case wrote:
> On Thu, May 26, 2011, Daniel Aiello wrote:
>
>> Therefore, we decided to run the same simulation using sander.MPI with
>> 16 processors. Below is the script I submitted to the SGE cluster to do
>> this. For comparison purposes, I am also running the serial version,
>> using a single processor. The processes for the sander.MPI job are
>> being distributed across 4nodes, each with 4 cores. Although, the
>> parallel job appears to be running faster than the serial job, the MPI
>> simulation runs for much longer than the estimated 5hr runtime, more
>> than a day, and is prone to hang ups. We are suspicious that the longer
>
> A better way to benchmark simulations is to run short simulations, since run
> time is just proportional to the length of simulation. In this way, you can
> quickly see how serial and parallel performance depends on number of
> processors, nodes, etc.
>
> Second, if you are looking at performance, using pmemd or pmemd.MPI should
> give much better behavior than sander.MPI. Is there a reason for you to be
> using sander?
>
> ....dac
>
>
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Received on Thu May 26 2011 - 10:00:04 PDT
