Re: MD Simulation of accelerated MD using GPU

From: Brian Radak (
Date: Mon Oct 12 2015 - 20:01:24 CDT

I am not an expert at all with the NAMD GPU implementation, but I would
suppose it is wholly possible that the added communication from
computing the potential energy at each step (since that defines the
boost factor) could slow down the simulation that much.


On 10/12/2015 05:19 PM, jeevan gc wrote:
> Dear all,
> In my protein membrane system of 121416 atoms,
> When I use 16 CPU +1 GPU, the total time is 3 days for 20ns for the regular MD.
> For the same system it takes 6 days to run 20ns accelerated MD.
> Why accelerated MD is slow in GPU? I am using NAMD2.10
> Thank you

Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812

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