[gmx-developers] Problem with g_covar diagonalizing large covariance matrices

Mendez Giraldez, Raul rmendez at email.unc.edu
Mon Oct 27 22:29:24 CET 2014

Hi Mark,

I've no idea about LAPACK compilation, Gromacs was installed in our computer cluster at UNC by the administrators.

Regarding my system, I do not include hydrogen atoms in the covariance computation, but if I am not wrong, they should not be a problem because they are constraints by LINCS. I have a homotetramer membrane channel protein, each monomer made of 226 residues (x4), in total about 14000 atoms protein only and about  1500 ions (that are close to the entrance top/bottom). The idea is to see whether low frequency modes of channel opening promote ion permeation. That's why I do not want to work with C-alpha only.

From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abraham at gmail.com]
Sent: Monday, October 27, 2014 3:48 PM
To: Discussion list for GROMACS development
Cc: Liu, Shubin; gromacs.org_gmx-developers at maillist.sys.kth.se
Subject: Re: [gmx-developers] Problem with g_covar diagonalizing large covariance matrices

On Mon, Oct 27, 2014 at 2:19 PM, Mendez Giraldez, Raul <rmendez at email.unc.edu<mailto:rmendez at email.unc.edu>> wrote:
Dear Gromacs developers,

I am trying to compute PCA on a 46464x46464 matrix (15488 atoms). g_covar produces segmentation fault. We thought it was a lack of physical memory, but when our computer cluster system administrator, Shubin Liu, looked into the system logs, found that the maximum RAM used by the program was 16 Gb, while I had booked up to 800 Gb of RAM. Shubin realized that the actual problem arises at the eigensolver call within covar routine. So it looks like eigensolver is unable to handle big matrices, but not because of lack of physical memory (is it based on LAPACK libraries, still 32-bit coded?).

I've no idea if there are any limits, but you can choose the LAPACK implementation with which to link GROMACS (see install guide), so you should find out what you've been using (e.g. inspect CMakeCache.txt in your build tree), and explore alternatives.

I am using Gromacs 4.6.3.

Do you know an alternative to that? The reason I want to do that is to have some ion atoms in addition to my protein and see how they move along the low frequency modes (large variance PCs).

How many of your protein atoms do you really need for that analysis? I presume you're already excluding the hydrogen atoms, since they're not doing much at low frequencies. Even if you think you really do need them, I suggest you start with something small that works.


Thank you so much,


Raul Mendez Giraldez, PhD
Dokholyan Lab
Dept. Biophysics & Biochemistry
Genetic Medicine
University of North Carolina
120 Mason Farm Road
Chapel Hill, NC 27599

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