Re: Non bonding energy calculation through NAMD

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Apr 12 2019 - 07:49:32 CDT

There are numerous tutorials on this as well as discussion in the user
guide -- I would recommend that you read these. The command line arguments
for multiple CPUs depends on the particular binary you are using and in
what context (multiple nodes, etc.), however the multicore version is the
simplest and most common:

$ namd2 +p<number of CPUs> <config file>

On Fri, Apr 12, 2019 at 3:29 AM varun dewaker <varun_dewaker1986_at_yahoo.com>
wrote:

> Dear Sir, CPU based calculation work fine, but it uses only single core.
> so it takes long time in interaction calculation . Kindly help me in
> sorting, how to instructs the NAMD energy program, so it uses all the cpu
> cores available.
>
> *Regards,*
> *Varun Kumar Dewaker*
> *Research Fellow*
> QSAR & Molecular Modelling Lab
> MPC Division (CSN-202)
> CSIR- Central Drug Research Institute
> Lucknow - 226031 (U.P), India
> *Mob:+918860194990*
>
>
> On Thursday, 11 April, 2019, 7:28:44 pm IST, Brian Radak <
> brian.radak_at_gmail.com> wrote:
>
>
> That message means just what it says - the pairInteraction keyword is not
> Cuda compatible. Try a CPU implementation.
>
> On Thu, Apr 11, 2019, 2:50 AM varun dewaker <
> varun_dewaker1986_at_remove_yahoo.com> wrote:
>
> Dear Sir
>
> I run the NAMD energy with NAMD multicore CUDA application. It says
> pair interaction calculation is not supported in CUDA version.
> What to do next?
>
> *Regards,*
> *Varun Kumar Dewaker*
> *Research Fellow*
> QSAR & Molecular Modelling Lab
> MPC Division (CSN-202)
> CSIR- Central Drug Research Institute
> Lucknow - 226031 (U.P), India
> *Mob:+918860194990*
>
>
> On Tuesday, 2 April, 2019, 7:34:23 pm IST, Giacomo Fiorin <
> giacomo.fiorin_at_gmail.com> wrote:
>
>
> Hi Varun, this calculation can be parallelized on CPU cores and/or GPU
> cores, as far as the NAMD executable you use supports it (i.e. you will
> probably want to use multicore-CUDA).
>
> To load a trajectory into NAMD directly without using VMD, take a look at
> coorfile:
>
> http://www.ks.uiuc.edu/Research/namd/2.13/ug/node9.html#SECTION00052200000000000000
>
> On Tue, Apr 2, 2019 at 5:02 AM varun dewaker <
> varun_dewaker1986_at_remove_yahoo.com> wrote:
>
> Dear NAMD users, my question is regarding the non-binding energy
> calculation. I want to calculate the non-binding energy from 26
> GB trajectory file generated by 100ns MD simulation.
>
> My first question is to confirm that this energy calculation runs only on
> a single processor or it is possible to run it on multicore or on GPU
> enabled system (since it takes a lot of time in the calculation).
>
> Another question is that it is possible to calculate non-binding energy
> without uploading the trajectories in the VMD.
> kindly suggest the syntax for this (without uploading the trajectories in
> VMD) since I am unable to upload all trajectories due to the limitation of
> RAM.
>
>
>
> *Regards,*
> *Varun Kumar Dewaker*
> *Research Fellow*
> QSAR & Molecular Modelling Lab
> MPC Division (CSN-202)
> CSIR- Central Drug Research Institute
> Lucknow - 226031 (U.P), India
> *Mob:+918860194990*
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
>

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