[gmx-users] computation/memory modifications

Justin Lemkul jalemkul at vt.edu
Sat Mar 10 18:28:12 CET 2018

On 3/9/18 1:17 PM, Mahmood Naderan wrote:
> Hi,
> I want to do some tests on the lysozyme tutorial. Assume that the tutorial with the default parameters which is run for 10ps, takes X seconds wall clock time. If I want to increase the wall clock time, I can simply run for 100ps. However, that is not what I want.
> I want to increase the amount of computation for every step, e.g. 1ps. Therefore I want another run for 10ps which takes Y seconds wall clock time where Y>X. I also want to increase the memory usage for each step compared to the default values in the tutorial.
> May I know which parameters are chosen for those purposes?

There aren't any, really. It's not in a user's interest to make GROMACS 
slower and less memory-efficient. You could presumably try to increase 
cutoff values, but I don't know if that will have a predictable impact 
on performance because then you're just shifting work from PME to 
short-range Coulombic forces.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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