[gmx-users] Memory issues using -ac option of gmx hbond

Smith, Micholas D. smithmd at ornl.gov
Mon Aug 7 23:53:31 CEST 2017

I had a similar problem. Using gromacs 2016.3's hbond tool fixed this. 

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Jared Sagendorf <sagendor at usc.edu>
Sent: Monday, August 07, 2017 5:46 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Memory issues using -ac option of gmx hbond

I'm trying to analyzing hydrogen bonds between a DNA and protein complex.
When using the -ac option of gmx hbond, I'm getting segmentation faults
which look like an out-of-memory problem.

However, I'm giving the process 64gb of memory, and an additional 64gb of
virtual memory. How memory intenstive is this program??

Note I am using version 5.1.13. A snippet of the output is below

Calculating hydrogen bonds between DNA_interface (919 atoms) and
Protein_interface (1026 atoms)
Found 138 donors and 458 acceptors
Making hbmap structure...done.
Found 117 different hydrogen bonds in trajectory
Found 156 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 117 to 116
- Reduced number of distances from 156 to 156
Average number of hbonds per timeframe 16.544 out of 31602 possible

D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
-------- -------- --- Thank You --- -------- --------

Doing autocorrelation according to the theory of Luzar and Chandler.
[hpc3338:34436] *** Process received signal ***
[hpc3338:34436] Signal: Segmentation fault (11)
[hpc3338:34436] Signal code: Address not mapped (1)
[hpc3338:34436] Failing at address: 0xfde7c370
[hpc3338:34436] [ 0] /lib64/libpthread.so.0(+0xf370)[0x7ff5c3810370]
[hpc3338:34436] [ 1]
[hpc3338:34436] [ 2]
[hpc3338:34436] [ 3]
[hpc3338:34436] [ 4]
[hpc3338:34436] [ 5]
[hpc3338:34436] [ 6] gmx_mpi(main+0xba)[0x40bfea]
[hpc3338:34436] [ 7]
[hpc3338:34436] [ 8] gmx_mpi[0x40be69]
[hpc3338:34436] *** End of error message ***

Am I doing something wrong here?
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