[gmx-users] NPT problem

[‪Mohammad Roostaie‬ ‪]

Hi All GROMACS users,


 
I created graphene with nanotube modeler then I created a force field for graphene based on OPLS (by using this link and its parameters: http://chembytes.wikidot.com/grocnt). I generated the topology file using x2top command. I put the graphene inside a box of water (TIP3P) which was larger than the graphene dimension with 1000  (kJ/mol nm^2) position restraint on all the atoms, and I performed the energy minimization and NVT equilibrations (in order to get an optimized structure of the graphene for further simulations). The results of both of them were good (energy level has reached a negative value with the order of 6 and the temperature has converged the preferred value). But, when I run the NPT equilibration, the results are not good (the pressure and density fluctuated very much and the averaged values are so far from the preferred ones). Also, during the NPT run, I received these messages:


step 53965: Water molecule starting at atom 127424 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141454: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141483: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323815: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323816: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323818: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355712: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355714: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355716: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355718: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469414: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469416: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469418: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469420: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
, and a pdb file was saved after each step.
In addition, something interesting is that I performed another run with all of the previous parameters, except I did not put position restraint on the graphene, and the results of NPT were good and acceptable, and I did not get those messages.


Can you please help me figure this problem out? Since I should put the position restrain on the graphene. I really would appreciate any help.


If you need further information please let me know.
Kind regards,Mohammad