Visualize the trajectory.

Hi,

How long did you run NVT, NPT? Can you share mdp files for NPT and md?

Your npt.gro file does not seem to be correct as the numbering is off, and box information is unavailable. Is it the complete gro file?

Water is not settled is generally due either to poor energy minimization, starting bad structure or poor mdp choices. Since you have successfully conducted the NPT, so it may be due to mdp options (but others can not be ignored).

If you are new, then follow a tutorial from Dr. Justin site. The choices are mostly fine to start and learn the md simulation.

http://www.mdtutorials.com/gmx/lysozyme/index.html

You need to pay attention to the cutoffs, if you are not following the force field used in the tutorial.

Good luck.

Ayaz Anwar

Hi,

I equilibrate the system 2ns for NVT and 10ns for NPT. I'll attach the npt.mdp file and md.mdp file. I use the same tutorial for simulation.

thank you

Hi,

Why did you turn the pressure coupling off in production run? Do you want to run under NVT conditions?

During NPT, you did not apply position restraints (-DPOSRES), its better (recommend) to apply in order to avoid the pressure (temperature) mediated structural changes.

why the comm-grps is only the DNA (why not DNA_protein)?

nstcomm should be >1, it slows down the simulation. The default value is 100, better apply that value

tc_grps is DNA water_and_ions (you do not have proteins in the system). Your npt.gro file contains protein molecules, why it is absent here.

tau_p and tau_t values are also suspicious; normally tau_t is 0.1, and tau_p is 2.0.

These are the few things I can see in your mdp files. Address these and see whether the production run shows the seg fault again.

Good luck.