# The system of protein-DNA was unstable and said "Segmentation fault" when i run NPT MD using gromacs **URL:** \ **Category:** User discussions\ **Tags:** forcefield, mdrun, simulation-setup\ **Created:** [January 25, 2024, 7:55am UTC](https://gromacs.bioexcel.eu/t/the-system-of-protein-dna-was-unstable-and-said-segmentation-fault-when-i-run-npt-md-using-gromacs/8136 "2024-01-25T07:55:13Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![xiangrui](https://avatars.discourse-cdn.com/v4/letter/x/ec9cab/32.png) [@xiangrui](https://gromacs.bioexcel.eu/u/xiangrui)\ **Post date:** [January 25, 2024, 7:55am UTC](https://gromacs.bioexcel.eu/t/the-system-of-protein-dna-was-unstable-and-said-segmentation-fault-when-i-run-npt-md-using-gromacs/8136/1 "2024-01-25T07:55:13Z")
GROMACS version: 2018.3 GROMACS modification: No Here post your question 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! ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [January 25, 2024, 8:09am UTC](https://gromacs.bioexcel.eu/t/the-system-of-protein-dna-was-unstable-and-said-segmentation-fault-when-i-run-npt-md-using-gromacs/8136/2 "2024-01-25T08:09:00Z")
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](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? ---
**Author:** ![xiangrui](https://avatars.discourse-cdn.com/v4/letter/x/ec9cab/32.png) [@xiangrui](https://gromacs.bioexcel.eu/u/xiangrui)\ **Post date:** [January 25, 2024, 9:22am UTC](https://gromacs.bioexcel.eu/t/the-system-of-protein-dna-was-unstable-and-said-segmentation-fault-when-i-run-npt-md-using-gromacs/8136/3 "2024-01-25T09:22:21Z")
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 ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [January 25, 2024, 10:16am UTC](https://gromacs.bioexcel.eu/t/the-system-of-protein-dna-was-unstable-and-said-segmentation-fault-when-i-run-npt-md-using-gromacs/8136/4 "2024-01-25T10:16:44Z")
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. ---
**Author:** ![xiangrui](https://avatars.discourse-cdn.com/v4/letter/x/ec9cab/32.png) [@xiangrui](https://gromacs.bioexcel.eu/u/xiangrui)\ **Post date:** [January 25, 2024, 10:31am UTC](https://gromacs.bioexcel.eu/t/the-system-of-protein-dna-was-unstable-and-said-segmentation-fault-when-i-run-npt-md-using-gromacs/8136/5 "2024-01-25T10:31:41Z")
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!