Re: water box and padding

From: Brian Radak (
Date: Mon May 02 2016 - 09:54:43 CDT

That's unfortunately a highly subjective request. There is no definitive
answer that I could speak of.

Some fairly objective experience - reducing the cutoff and switch
distance while using an LJcorrection can give ~10% speedup without
statistically changing NpT quantities, at least for small water boxes. I
couldn't say what this will do for heterogenous protein and/or membrane
systems (there have been some papers on this in the last decade or so).


On 04/30/2016 11:40 AM, Dhiraj Srivastava wrote:
> Hi all
> whats the minimum padding that I should use without
> compromising with the results of simulation? when I am using 10 A
> padding then I am getting more than 200,000 atoms and in our machine
> with GPU, I can only get 3 ns / day. I want to speed up the
> calculation without compromising with the results. Can I go upto 5 A
> padding?
> Thanks
> Dhiraj

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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