Hi, Mark,
I'd be happy to, as soon as I get a chance.
I know very little about how GROMACS works internally, but I had a few
ideas I wanted to share in the hopes that they might help. One is that
pairwise parameters for electrostatics could be implemented in the same way
that LJ parameters are
Hi,
I don't have a solution for the question at hand, but it'd be great to have
your inputs attached to a new issue at https://redmine.gromacs.org, so that
we can have such an input case to test with, so that we can improve the
simplistic implementation! Please upload it if you can.
Mark
On
Scratch that comment about sparseness. I am short on sleep, and for a
moment thought I was talking about constraints, not electrostatics.
On Fri, Mar 8, 2019 at 1:12 PM Sean Marks wrote:
> I understand now, thank you for the prompt response. While the matrix
> would actually be quite sparse
I understand now, thank you for the prompt response. While the matrix would
actually be quite sparse (since the constraints are localized to each ice
molecule), I take it that memory is being allocated for a dense matrix.
That aside, is it feasible to accomplish my stated goal of scaling
On 3/8/19 11:04 AM, Sean Marks wrote:
Hi, everyone,
I am running into an issue where grompp is using a tremendous amount of
memory and crashing, even though my system is not especially large (63976
atoms).
I am using GROMACS 2016.3.
My system consists of liquid water (7,930 molecules) next
Hi, everyone,
I am running into an issue where grompp is using a tremendous amount of
memory and crashing, even though my system is not especially large (63976
atoms).
I am using GROMACS 2016.3.
My system consists of liquid water (7,930 molecules) next to a block of ice
(8,094 molecules). The
