14 November 2019 10 6K Report

I'm waiting on email conformation for the GMX user group, but this is in reply to Reviewers so I'm pressed for time and asking here.

I'm building a small collagen-based system. The crystal structure dimensions are:

15.91920 2.58660 2.70113 0.00000 0.00000 0.00000 0.00000 -0.18557 0.00000

I'm using Gromacs version 2016.4 - I can't change this as it's what's installed on the work server.

I've built this system before (with slight changes) and I've never had these problems. I keep getting segmentation faults when running gmx mdrun. There is no output in the .log file beyond the system configuration output. I do, however, see the Tolerance (Fmax) and Number of steps before mdrun dies.

My execution line:

gmx mdrun -deffnm enrun -rdd 1 -nt 1 -pin on

Non-verbose screen output:

Back Off! I just backed up enrun.log to ./#enrun.log.3#

Running on 1 node with total 24 cores, 24 logical cores

Hardware detected:

CPU info:

Vendor: Intel

Brand: Intel(R) Xeon(R) Gold 6126 CPU @ 2.60GHz

SIMD instructions most likely to fit this hardware: AVX_512

SIMD instructions selected at GROMACS compile time: SSE2

Hardware topology: Only logical processor count

Compiled SIMD instructions: SSE2, GROMACS could use AVX_512 on this machine, which is better.

Reading file enrun.tpr, VERSION 2016.4 (single precision)

Using 1 MPI thread

Using 1 OpenMP thread

At the moment my geometry file does not contain water. That's fine - I was just testing my geometry at this stage. However, when I try solvating the system with:

gmx solvate -cp test.gro -cs spc216.gro -p system.top -o solvated2.gro

I get another segmentation fault:

Reading solute configuration

CRYSTAL STRUCTURE OF COLLAGEN-LIKE PEPTIDE AT 1.27 ANGSTROM

Containing 7822 atoms in 640 residues

Reading solvent configuration

216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984

Containing 648 atoms in 216 residues

.....

Generating solvent configuration

Will generate new solvent configuration of 9x2x2 boxes

Solvent box contains 13827 atoms in 4609 residues

Removed 3036 solvent atoms due to solvent-solvent overlap

Segmentation fault

The fact that gmx solvate crashes is a lot more revealing than gmx mdrun. I'm just a little unsure of how to troubleshoot these issues?

Much appreciated. Thanks.

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