[gmx-users] Speeding up simulation

[Justin A. Lemkul]

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

========================================