Re: Non bonding energy calculation through NAMD

From: varun dewaker (varun_dewaker1986_at_yahoo.com)
Date: Fri Apr 12 2019 - 02:29:06 CDT

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 DewakerResearch FellowQSAR & Molecular Modelling LabMPC Division (CSN-202)CSIR- Central Drug Research InstituteLucknow - 226031 (U.P), IndiaMob:+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 DewakerResearch FellowQSAR & Molecular Modelling LabMPC Division (CSN-202)CSIR- Central Drug Research InstituteLucknow - 226031 (U.P), IndiaMob:+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 DewakerResearch FellowQSAR & Molecular Modelling LabMPC Division (CSN-202)CSIR- Central Drug Research InstituteLucknow - 226031 (U.P), IndiaMob:+918860194990

-- 
Giacomo FiorinAssociate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
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