Re: Non bonding energy calculation through NAMD

From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Apr 12 2019 - 14:02:34 CDT

As an alternative, you can start namdenergy with the -debug flag set
(either via the command line or GUI interface), but then kill the namd job
that it spawns, and then namd yourself instead. Behind the scenes it just
writes some temporary files to your working directory that can be run using
whatever combination of namd commands you wish.
Best,
Peter

On Fri, Apr 12, 2019 at 2:51 PM Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:

> You can modify the source code of the NAMD energy plugin. Find the line
> where it actually runs NAMD and change it to correspond to what you want
> (+p<number of CPUs>).
>
> Best,
> JC
>
> On Apr 12, 2019, at 9:58 AM, Brian Radak <brian.radak_at_gmail.com> wrote:
>
> 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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