Hi, so I modified my mdp file which now looks like the following: title = production MD ; Run parameters integrator = md ; leap-frog algorithm ;nsteps = 20000000 ; 0.005 * 20000000 = 100000 ps or 100 ns ;nsteps = 200000 ; 0.005 * 200000 = 1 ns ;dt = 0.005 ; 5 fs 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 ; 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) cutoff-scheme = Verlet ; 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 --------------------------------------------------
But, when I try to generate the tpr file on the cluster itself using gromacs 4.6.3, I get the following error: NOTE 1 [file md3.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 md3.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Generated 3403 of the 3403 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3403 of the 3403 1-4 parameter combinations Segmentation fault Can anyone please suggest further? Kind regards, Ankita On Mon, Mar 24, 2014 at 11:48 AM, Ankita Naithani <ankitanaith...@gmail.com>wrote: > 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 > -- 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? 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