This is a very common post on previous mailing list however, I am still not able to fix the problem of position restraints during NPT.
I have a carbon nanotube aligned to z-direction. I am trying to simulate infinite nanotube using periodic conditions. It is common to use position restraints for nanotube (most papers report this). I have imposed position restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1 nm. This is not an issue with NVT simulation (Berendsen thermostat and barostat). I tried different thermostats and barostats, they deform the nanotube as previously discussed on gromacs mailing list. How do I equilibrate nanotube system with position restraints when used together with pressure coupling? Should I play with the box size after first NVT run? The force field is opls based on gromacs guideline on CNTs and GROMACS version is 5.1.4. The mdp parameters are below: Thank you in advance, Sincerely, Neha title = OPLS Lysozyme NPT equilibration define = -DPOSRES_CNT ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 500000 ; 2 dt = 0.001 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 1.0 ps nstvout = 5000 ; save velocities every 1.0 ps nstenergy = 5000 ; save energies every 1.0 ps nstlog = 5000 ; update log file every 1.0 ps ;energygrps = Protein CNT Water NA ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Berendsen ; modified Berendsen thermostat tc-grps = CNT Water ; two coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Berendsen ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 5.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC periodic_molecules = yes ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off -- Regards, Dr. Neha S. Gandhi, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.