The system of protein-DNA was unstable and said "Segmentation fault" when i run NPT MD using gromacs

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1

GROMACS version: 2018.3
GROMACS modification: No
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I run a simulation of protein-DNA using gromacs with amber14sb_parmbsc1 force field. The structure was got from X-ray crystal structure. I did energy minimization, 1 ns equilibration of NVT and NPT. When I run production MD, the system stopped about after 5 ns, and said "Segmentation fault ". I check the structure and mdp file, do not find wrong. Can you help me? Thank you!

2

A segmentation fault is not desirable - a more elegant crash would be nicer. But what you are experiencing is almost certainly that the system is unstable, see https://manual.gromacs.org/current/user-guide/terminology.html#blowing-up for more information.

The first thing I would try is to make sure that the system is properly energy minimized. I would then extend the equilibration simulations, e.g. to 2 ns NVT and 2 ns NPT. If that does not help I would have a close look at the simulation parameters. Are you thermostat and barostat settings good?

3

Dear Mr. Magnusl
Thank you for your nice suggestion.
The detailed information of the parameters I set is as follows. I set “emtol=50.0” when I do energy minimization and it converged. I used “V-rescale” as thermostat and “Berendsen” as barostat at the stage of equilibration. The “V-rescale” and “Parrinello-Rahman” was used at production MD, and tau_t=0.2, tau_p=2.0.
I will try to extend the equilibration simulations. I have a new question. Is prolonging the tau_p useful for maintaining system stability?
Looking forward to your reply.

The following is md.mdp:

integrator = md
dt = 0.002 ; ps
nsteps = 5000000 ; 10ns
comm-grps = DNA_Protein
comm-mode = angular
;
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 5000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-grps = system
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
DispCorr = EnerPres
;
Tcoupl = V-rescale
tau_t = 0.2 0.2
tc_grps = DNA_Protein Water_and_ions
ref_t = 298.15 298.15
;
Pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
;
constraints = hbonds

4

Nowadays, I would recommend using the c-rescale barostat instead of berendsen and parrinello-rahman, but that was not available in GROMACS 2018.

However, I would suggest using tau_t=1.0 (for all temperature coupling groups) and tau_p=5.0 - parrinello-rahman might require even higher. That might help with the stability.

5

Dear Mr. MagnusL
Thanks so much for your help.
I am very pleased to receive your suggestions. I will take your suggestions and try them on my system.
Thank you!