[gmx-users] Speeding up simulation

[ms]

On 17/08/10 22:36, Justin A. Lemkul wrote:

> 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.

This interests me -I've used simple cut-off for in vacuo tests, but I 
still hadn't made my mind on what electrostatic model I should truly 
use. Do you have any suggestion?

thanks,
M.

> 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
>>
>