[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

Thanks for your help.


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
> 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

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