Re: Non bonding energy calculation through NAMD

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Apr 02 2019 - 09:00:54 CDT

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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