Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; 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 = 1.0 ; short-range van der Waals cutoff (in nm) rlistlong = 1.0 ; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet
But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar <kumar.pavan...@gmail.com>wrote: > Hello Ankita > You have to just include the following line in your mdp file > cutoff-scheme=Verlet > And run your grompp with the modfied mdp file to generate tpr file and then > mdrun. > Hope this doesn't give you the same error > > > On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani > <ankitanaith...@gmail.com>wrote: > > > Hi, > > > > I am trying to run a simulation of my protein (monomer ~500 residues). I > > had few questions and erors regarding the same. > > I have previously run the simulation of the apo form of the same protein > > using Gromacs 4.5.5 which was available at the cluster facility I was > using > > and also which is installed in my system. However, when I tried to run > the > > holo form, I got error : > > Fatal error: > > 11 particles communicated to PME node 106 are more than 2/3 times the > > cut-off out of the domain decomposition cell of their charge group in > > dimension y. > > This usually means that your system is not well equilibrated. > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > This I figured out could be solved using a lower timestep as my previous > > timestep was 4fs and now I have reduced it to 3fs which should work fine > > now. > > However, after producing the tpr file for production run in my GROMACS > > 4.5.5, I realised that the grant for the cluster facility is over and the > > new clusters which I am trying to set up the same protein for support > only > > gromacs 4.6. I am trying to run the code in these clusters and I get he > > following error: > > > > > > ------------------------------------------------------- > > Program mdrun_mpi, VERSION 4.6.3 > > Source code file: /home/gromacs-4.6.3/src/kernel/runner > > .c, line: 824 > > > > Fatal error: > > OpenMP threads have been requested with cut-off scheme Group, but these > are > > only > > supported with cut-off scheme Verlet > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > > --------------------------------------------------------------------------------- > > > > 1. I wanted help with my mdp options to make it compatible. > > 2. Since my pevious calculations were based on gromacs 4.5.5, switching > to > > gromacs 4.6, would that break the continuity of the run or would that > bring > > about differences in the way the trajectories would be analysed? > > > > > > Below, is my mdp file > > title = production MD > > ; Run parameters > > integrator = md ; leap-frog algorithm > > nsteps = 33333333 ; 0.003 * 33333333 = 100000 ps or 100 n > > dt = 0.003 ; 3 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 > > energygrps = Protein ATP > > ; Bond parameters > > 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 > > 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 = 1.0 ; short-range van der Waals cutoff (in nm) > > rlistlong = 1.0 ; long-range neighborlist 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 > > 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 = berendsen ; Berendsen thermostat > > pcoupltype = isotropic ; uniform scaling of box vectors > > tau_p = 1.0 ; 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 > > > > > > > > > > Kind regards-- > > 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. > > > > > > -- > Cheers > Pavan > -- > 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. > -- 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.