Dear all, I am trying to study an infinite length CNT in SPC water box under NPT using gromacs 4.5.3. The axis of CNT is along Z direction. The options "pbc = xyz " and "periodic_molecules = yes" are included in all mdp files. The whole system was minimized first, followed by an NVT simulation. The structure was fine, at least when visualized with VMD. Then I ran an NPT simulation with weak restraint on CNT. The pressure coupling options are set as following ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of box vectors tau_p = 2.0 0.0 ; time constant, in ps ref_p = 1.0 0.0 ; reference pressure, in bar compressibility = 4.5e-5 0.0 ; isothermal compressibility of water, bar^-1
And the final structure was also fine. But then I removed the constraint, and tried to run a long time simulation under NPT, the whole system exploded in several ps. I have not figured out what was wrong in my calculation. Can anyone give me a suggestion? Ye MEI -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
