[gmx-users] Segmentation fault during equilibration

[Mark Abraham]

Hi,

As normal, even for coarse-grained simulations, equilibration may require
bigger rearrangements for some starting conditions than others. The usual
advice for http://www.gromacs.org/Documentation/Terminology/Blowing_Up still
applies - particularly to try smaller time steps while relaxing what might
be large forces.

You could also compile better to suit this machine and get higher
performance ;-)

Mark

On Tue, Feb 23, 2016 at 5:06 PM Yasser Almeida <
yasser.almeida.hernandez at chemie.uni-hamburg.de> wrote:

> Hi all,
>
> I am running an equilibration of a membrane/protein coarse grained
> system and got this Segmentation fault error.
>
> ---
> Reading file equilibration.protein_DPPC.tpr, VERSION 4.6.5 (single
> precision)
> Using 8 MPI threads
> Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this
> machine, which is better)
> starting mdrun 'Protein in INSANE! Membrane UpperLeaflet>DPPC=1
> LowerLeaflet>DPPC=1'
> 25000 steps,    500.0 ps.
> step 0
> Step 3, time 0.06 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000001, max 0.000003 (between atoms 204 and 205)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       30     31   32.7    0.1950   0.1950      0.1950
>
> Step 4, time 0.08 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 195678.573993, max 1044637.687500 (between atoms 30 and 31)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       30     31   90.0    0.1950 203704.5469      0.1950
> Wrote pdb files with previous and current coordinates
> Segmentation fault (core dumped)
> ---
>
> This is the mdp file:
> ---
> dt         =  0.02
> nsteps       =  25000
> nstxout      =  0
> nstvout      =  0
> nstlog       =  100
> nstxtcout     =  100
> xtc-precision     =  100
> rlist         =  1.4
> coulombtype     =  shift
> rcoulomb     =  1.2
> epsilon_r     =  15
> vdw-type     =  shift
> rvdw-switch     =  0.9
> rvdw         =  1.2
> tcoupl       =  v-rescale
> tc-grps      =  Protein_DPPC W_Ion
> tau-t         =  1.0 1.0
> ref-t         =  323 323
> Pcoupl       =  berendsen
> Pcoupltype     =  semiisotropic
> tau-p         =  10.0 10.0
> compressibility  =  3e-4 3e-4
> ref-p         =  1.0 1.0
> refcoord_scaling =  com
> ---
>
> I've used this settings before with similar protein/membrane systems
> without problem.
>
> Any thoughts?
> Thanks in advance
>
> Yasser
>
> --
> Yasser Almeida Hernández
> PhD student
> Institute of Biochemistry and Molecular Biology
> Department of Chemistry
> University of Hamburg
> Martin-Luther-King-Platz 6
> 20146 Hamburg
> Germany
> +49 40 42838 2845
> yasser.almeida.hernandez at chemie.uni-hamburg.de
> office: Grindelallee 117, room 250c
>
> --
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