[gmx-users] Speeding up simulation

sapna sarupria sapna.sarupria at gmail.com
Tue Aug 17 23:33:59 CEST 2010


Hi Justin
Thanks for your response. I suspect that it is the same thing. Is there a
way to make gromacs use PME only within a certain region of the simulation
box? Also, how does one know how to fix the load imbalances (in this
context)?

Thanks for your help.

Sapna

On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> sapna sarupria wrote:
>
>> Hi all,
>>
>> I am running (NVT) simulations of a drop of water (~5 nm in radius) in a
>> big box (~25 nm) in a box and find that the simulations are rather slow. I
>> am getting about 0.8 ns per day when a simulation of bulk system of
>> equivalent number of waters will be much faster. The number of waters is
>> ~12000. I was wondering if anyone can suggest methods with which I can speed
>> up the simulations. I am using domain decomposition and optimize_fft is set
>> to yes. PME is used for the electrostatics.
>>
>
> I would suspect that the lag comes from a lot of unused PME calculations.
> During your run, PME grid points will be assigned to vacuum space, for which
> nothing needs to be done.  You can check imbalances and performance loss in
> the log file.
>
> -Justin
>
>
>> Thank you
>>
>> Sincerely
>> Sapna
>>
>>
> --
> ========================================
>
> 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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-- 
Sapna Sarupria
Post-doctoral Researcher
Princeton University
New Jersey 08540
U.S.A.

Life isn't about finding yourself. Life is about creating yourself. --
George Bernard Shaw.
Dare to Dream
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