[gmx-users] Speeding up simulation

[Gaurav Goel]

Sapna,

Is there a particular reason you're using a box so much larger than the
droplet diameter? If your only concern is that periodic images should not
see each-other maybe you can use a box length=droplet diameter+2*largest
cut-off in the system.

Also using a more spherical box shape such as  rhombic dodecahedron or the
truncated octahedron will help you in reducing the volume of unfilled space.

-Gaurav

On Tue, Aug 17, 2010 at 5:40 PM, sapna sarupria <sapna.sarupria at gmail.com>wrote:

> 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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