[gmx-developers] MC with PME

[Berk Hess]

Floris Buelens wrote:
>> Furthermore, I implemented functionality to calculate the PME mesh
>> energy at a single location only. This makes the PME cost for multiple
>> trial moves nearly identical to a single PME evaluation.
>>     
>
> Can you elaborate on this? Could this be applicable to free energy with PME, where A and B states each require a full PME evaluation?
>   
This code is used in src/mdlib/tpi.c.
It would only be useful for free-energy if you change a single charge is
the system,
since with multiple charges the changing charges affect the potential in
a complicated way.

Berk
>
>
>
> ----- Original Message ----
> From: "hess at sbc.su.se" <hess at sbc.su.se>
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Sent: Mon, 14 June, 2010 22:45:22
> Subject: Re: [gmx-developers] MC with PME
>
>   
>> On 2010-06-14 21.09, André Assunção S. T. Ribeiro wrote:
>>     
>>> Dear all,
>>>
>>> I have been working to implement a Monte Carlo "integrator" for GROMACS.
>>> For the last couple of months I've been trying to improve performance of
>>> the algorithm. For that end, I have made adaptations to the ns and force
>>> evaluation routines. Energies for each interaction are stored
>>> separately, so one can just calculate the needed energy terms in each
>>> trial move. When treating nonbonded interactions with a cutoff, MC
>>> performance is more than 10-fold greater than MD for a simple system
>>> containing 216 SPC waters (by performance I mean number of simulation
>>> steps/CPU time, not actual sampling efficiency). When I use PME, the
>>> situation is far worst, with an approximate 3-fold increase. When I try
>>> to call gmx_pme_do for only a small number of atoms performance
>>> decreases when compared to the total calculation. For simple Ewald sum,
>>> there is a 10-fold increase when a single molecule is calculated,
>>> however, it is still a lot slower than the worst PME result. Would
>>> anyone have any ideas on how to increase performance here?
>>>       
>> If you use MC you do not need to evaluate forces, this will remove 30%
>> of the PME time roughly. It used to be coded in there at some stage, but
>> it might have been removed.
>>
>>     
>
> Furthermore, I implemented functionality to calculate the PME mesh
> energy at a single location only. This makes the PME cost for multiple
> trial moves nearly identical to a single PME evaluation.
> But I would still think it is far more expensive than MD,
> since you move only one or a few particles at a time.
>
> Berk
>
>   
>>> Cheers,
>>> Andre.
>>>
>>>       
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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>>     
>
>