Re: Non bonding energy calculation through NAMD

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Apr 12 2019 - 08:58:45 CDT

I haven't worked extensively with the NAMDEnergy plugin -- I would consult
the VMD plugin documentation or ask that question on the vmd-l listserv.

On Fri, Apr 12, 2019 at 9:24 AM varun dewaker <varun_dewaker1986_at_yahoo.com>
wrote:

> Dear Sir
> 1. Using NAMDEnergy plugin I am calculating Nonbond energy between
> selection-1 (protein) and selection-2 (ligand) from MD trajectories.
> 2. Under default setup NAMDEnergy plugin is using single core for this
> computation.
> 3. Following is My question:
> How to activate multicore processing/processors to calculate Nonbond
> energy between selection-1 (protein) and selection-2 (ligand) from MD
> trajectories in NAMDEnergy plugin?
>
> Thanks in advance.
>
> *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 Friday, 12 April, 2019, 6:21:30 pm IST, Brian Radak <
> brian.radak_at_gmail.com> wrote:
>
>
> 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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