[gmx-users] Speeding up simulation

[sapna sarupria]

Hi Justin

Thanks for your input. I guess I will do some more literature search and try
to optimize the simulations as much as I can.

Thanks,
Sapna

On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> sapna sarupria wrote:
>
>> 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)?
>>
>
> There is no way to limit PME to certain ranges.  It is a method for solving
> infinite sums.  Usually PME is a poor choice for in vacuo simulations and
> the like, since there's nothing to be done for most of the simulation box.
>  You may want to see how others (in the literature) deal with droplet-type
> simulations.
>
> -Justin
>
>
>> Thanks for your help.
>>
>> Sapna
>>
>> On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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 <http://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
>>
>>
> --
> ========================================
>
> 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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