VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 28 2016 - 00:21:34 CST

Hi,
  I'm not sure if you got your answer already on the NAMD-L list, but
just for future reference, the NAMD config files for GPU-accelerated runs
are generally the same as those for CPU-based runs except that you want to
ensure that you are not doing things such as outputting energies, saving
trajectory timesteps, or writing restart files or other non-GPU-work
at an indordinately high frequencies, as such things will end up slowing
down the simulation since they prevent the GPU from running at full speed.
The best thing is to inquire on the NAMD-L mailing list for a more complete
answer, but I wanted to write a brief answer here in case anyone else
eventually searches for this topic on VMD-L.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Nov 20, 2016 at 01:18:43PM +0500, Naeem Mahmood Ashraf wrote:
> Hi,
> Is there anyone who is currently using GPU to run simulations. I am new to
> GPU and need the little help to prepare the conf file to run a simulation
> on GPU. Can we use CPU conf file in GPU?
> Thanking in anticipation
> --
> Naeem Mahmood Ashraf
> Lecturer Biochemistry & Molecular BiologyA
> University of Gujrat, PunjabA
> Cell Number: +923355064805
> E-mail: [1]naeem.mahmood_at_uog.edu.pkA
>
> References
>
> Visible links
> 1. mailto:naeem.mahmood_at_uog.edu.pk 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/