Re: Non bonding energy calculation through NAMD

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Apr 12 2019 - 13:04:16 CDT

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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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

This archive was generated by hypermail 2.1.6 : Fri Dec 06 2019 - 23:20:36 CST