Hi, I am trying to run a simulation with the following optins in my production mdp file. Previously I have run the simulations with the production run parameters using V-rescale thermostat and berendsen barostat. But now recently I read in discussion that Justin had advised using Parinello-Rahman barostat as it would be much more suitable and provides adequate sampling. Also, I had to use the Verlet cut-off scheme because the cluster where I run my production simulation has updated gomacs to the recent version 4.6.5 which requires one to use the verlet scheme.
My mdp file is below title = production MD ; Run parameters integrator = md ; leap-frog algorithm nsteps = 50000000 ; 0.002 * 50000000 = 100000 ps or 100 ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 2 ps nstvout = 0 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 5 ps nstenergy = 1000 ; save energies every 5 ps nstlog = 1000 ; update log file every 5 ps ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constraine d lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 25 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) rlistlong = 1.0 ; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostat ics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT nstcomm = 10 ; remove com every 10 steps ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 318 318 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = Parrinello-Rahman ; pressure coupling is on for NP T pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 318 ; reference temperature, for protein in K ERROR 1 [file md.mdp]: With Verlet lists rcoulomb!=rvdw is not supported NOTE 1 [file md.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file md.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy WARNING 1 [file md.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. Velocities were taken from a Maxwell distribution at 318 K Removing all charge groups because cutoff-scheme=Verlet There were 2 notes There was 1 warning ------------------------------------------------------- Program grompp_d, VERSION 4.6.5 Source code file: /home/y07/y07/gmx/4.6.5-phase1/source/src/kernel/grompp.c, line: 1610 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- So, I guess, NOTES 1 and 2 are harmless and can be ignored, right? Regarding error 1, I think I would have to change my rvdw to 1.0 and that should sort the problem out. I wanted to get advice on the warning too, should I ignore and proceed? Or should I go back to berendsen as I have been using for my previous simulations. For NVT and NPT, I have used berendsen. As this is a very crucial simulation run, I just wanted to confirm since I have not had any previous experience with Parinello-Rahman so, any advice would surely help me. -- Ankita Naithani -- 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.