I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as
tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee < ananyachatter...@iiserkol.ac.in> wrote: > Hi all, > > I was running a md simulation of protein complexed with GTP in water, > neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol > and also equilibrated the water molecules in 300K temperature and 1 bar > pressure. And then run the md simulation using md parameters as follow: > > title = Protein-ligand complex > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 500000 ; 2 * 5000000 = 1000 ps (1 ns) > dt = 0.002 ; 2 fs > ; Output control > nstxout = 500 ; save coordinates every 1ps > nstvout = 500 ; save coordinates every 1ps > nstenergy = 500 ; save energies every 1 ps > nstlog = 500 ; update log file every 1 ps > nstxtcout = 500 ; write .xtc trajectory every 1 ps > energygrps = Protein GTP SOL MG2+ > ; Bond parameters > constraints = none ; No constrains > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > rlist = 0.9 ; short-range neighborlist cutoff (in nm) > rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) > rvdw = 1.4 ; short-range van der Waals cutoff (in nm) > ; Temperature coupling > tcoupl = v-rescale ; modified Berendsen thermostat > tc-grps = Protein GTP SOL MG2+ CL- ; two coupling groups - more > accurate > tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps > ref_t = 300 300 300 300 300 ; reference temperature, one > for each group, in K > ; Pressure coupling > pcoupl = Parrinello-Rahman ; pressure coupling is on for > NPT > 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 > refcoord_scaling = com > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > > > Now I am getting the following error. > > > Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is > larger than the 1-4 table size 2.400 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > > t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. > Check for bad contacts and/or reduce the timestep. > Wrote pdb files with previous and current coordinates > > ------------------------------**------------------------- > Program mdrun, VERSION 4.0.7 > Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 > > Fatal error: > Number of grid cells is zero. Probably the system and box collapsed. > > kindly help me I am not getting where I am getting wrong. > > > > -- > Ananya Chatterjee, > Senior Research Fellow (SRF), > Department of biological Science, > IISER-Kolkata. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
