[gmx-users] Speeding up simulation

[Gaurav Goel]

Large cut-offs can bring artificial artifacts.

e.g. *Chemical Physics
Letters*<http://www.sciencedirect.com/science/journal/00092614>
 Volume 406, Issues
1-3<http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%235231%232005%23995939998%23591997%23FLA%23&_cdi=5231&_pubType=J&view=c&_auth=y&_acct=C000062818&_version=1&_urlVersion=0&_userid=6325866&md5=51f91ba17c3ce282da206786a17d50d5>,
23 April 2005, Pages 49-53

-Gaurav

On Wed, Aug 18, 2010 at 12:04 PM, sapna sarupria
<sapna.sarupria at gmail.com>wrote:

> That might actually be the best approach speed wise. But it depends on what
> level of accuracy you wish for your calculations. What is your system like?
> May be you can have a large cut off but you will have to see what the trade
> off between speed and accuracy is.
>
>
> On Wed, Aug 18, 2010 at 10:26 AM, ms <devicerandom at gmail.com> wrote:
>
>> 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
>>>>
>>>>
>>>
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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
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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