Dear gromacs user I did simulation of carbon nanotube (one in center and 6 in the vicinity of that)|:
every CNT have 120 atoms. 1) energy minimization 2) equilibration in NVT ensemble when I did equilibration in NPT ensemble, I encountered Fatal error: Number of grid cells is zero. Probably the system and box collapsed. How to solve this problem (with which parameter in the mdp file I can solve this problem)? Is there problem in the force field parameters? If this problem resolves, can I do simulation under these conditions but in the high pressure or tempreture (800 bar or 1800 K)? mdp file for equilibration in NPT ensemble is as follows: title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.001; ps ! nsteps = 50000 ; total (2 ns). nstcomm = 1 nstxout = 100 nstxtcout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 0.8 rcoulomb = 0.8 rvdw = 0.8 ; Electrostatics coulombtype = Cut-off ; vdw vdwtype = Cut-off ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc-grps = (NU center tau_t = 0.10 0.10 ref_t = 1300 1300 ; Energy monitoring energygrps = (NU center ; Isotropic pressure coupling is now on Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1 ; Generate velocites is off at 1300 K gen_vel = no ; Periodic boundary conditions pbc = xyz ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 90 ; Non-equilibrium MD freezegrps = (NU center freezedim = N N N Y Y Y Any help will highly appreciated. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
