Re: NAMD+PLUMED

From: jing liang (jingliang2015_at_gmail.com)
Date: Sun Jun 03 2018 - 05:15:09 CDT

Hi,

thanks for your comments, they are insightful. I am cc'ing this message to
your emails (you may receive this message twice) let me
know if this is the common procedure or just replying to namd-l.

Being more specific, I tried a water box ~40A with two Na+ and Cl- ions and
used the distance between them to get the PMF using
Metadynamics (standard and well-tempered) and Colvars. Just now, I realized
that my script is performing faster with GPU if I use the
following scheme:

namd2 +p28 metadynamics.inp

previously, I used +p1, I thought it was required by NAMD-GPU version. With
the scheme above, the GPU version runs 1.6 times
faster than the same scheme on CPUs (50,000 steps).

I just wonder, on what set of conditions PLUMED would run faster than
Colvars, i.e. system size, number of CVs, etc.? Or maybe
PLUMED is better suited for CVs that are not supported by Colvars?

Thanks.

2018-06-03 5:03 GMT+02:00 Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>:

> Just my two cents: PLUMED and Colvars both effectively ignore the GPU, and
> only do the calculations on the CPU. The rest of the MD dynamics will use
> GPUs as appropriate, but if your collective variable isn't reasonable, it
> may well end up bottlenecking performance with both codes.
>
> -Josh
>
>
>
> On 2018-06-02 15:31:08-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Hi, the use of GPUs is supported with either code, in that the GPU-enabled
> version of NAMD can run with either Colvars, or PLUMED if you specifically
> compile it with NAMD.
> The error you saw was probably unrelated to the combination of Colvars,
> metadynamics and GPU.
> As for the performance, you need to give some specifics regarding, the
> type of system and the type of collective variables, and the hardware you
> plan on running on, to get useful advice.
> Regards,
> Giacomo
>
> On Sat, Jun 2, 2018 at 2:34 PM, jing liang <jingliang2015_at_gmail.com>
> wrote:
>>
>> Hi,
>> I tried to run a Metadynamics simulation in NAMD using Colvars on a GPU
>> card but it seems that this type of simulations is not supported yet on
>> GPUs,
>> right?
>> Then, I read about an alternative for Colvars called PLUMED. Do you know
>> if NAMD+PLUMED can be run on GPUs?
>> Compared to Colvars, does PLUMED runs faster or scales better with the
>> number of cores for instance?
>> Any comment is welcome.
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
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>

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