[gmx-users] A question on execusion speed

[Justin A. Lemkul]

Paymon Pirzadeh wrote:
> Hello,
> I have question regarding the execution time of a trajectory. I used to
> run my trajectory at 265K or 275K and at the end of the log file the
> speed was reported as e.g. 1.18 ns/day. Recently, I changed the
> temperature to 288K and now my simulation is not finished in the
> assigned wall time (240 hours). The potential and total energy and other
> parameters in the log file looks fine. Is there really sth going on with
> temperature or the cluster I am running the jobs on?!

I can't think of a reason why simply changing the temperature would drastically 
alter the speed of the simulation.  Look to the hardware.  When I've had random 
decreases in performance, it's because a node is having issues or the 
interconnect is bugging out.

-Justin

> Regards,
> 
> Paymon 
> 

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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