Hi, I am simulating a Martini coarse grained DNA protamine system. I have 1 infinite DNA + 1 protamine. Since while using the martini python script for coarse graining it removes the 2 phosphate atoms of the terminal base pairs, so in order to have the right infinite DNA system, while building it, I had build 2 extra base pairs, which I removed them manually and renumbered the topology .itp file atom numbers to match with the .gro file. So my periodic cuboidal box size in Z direction (the DNA is aligned along Z) is # of BPs*3.38 Angstrom, so that the pbc along Z makes the DNA infinite.
The problem is when I simulate this system, during the short NPT equilibration, it shows this error : Fatal error: symtab get_symtab_handle 367 not found The strange thing is if I submit a short run, in interactive mode for eg, it runs fine, as long as it stays connected. But when I submit the complete run in the cluster, it shows this error, before even starting Step 0. I tried to google about this error, but didn't find much info. I have been running this simulation in version 5.0.6. I checked also using newer version of gromacs 5.1.4, it shows running status, but in the .log file it shows this : Started mdrun on rank 0 Thu Jun 14 01:29:37 2018 Step Time Lambda 0 0.00000 0.00000 Not all bonded interactions have been properly assigned to the domain decomposition cells Are the 2 different errors that I get in the different versions, connected? To test if there is a problem in the force field (.itp file) since I had to modify it manually to renumber the atoms, I ran a finite 50 BP DNA with modified .itp file for the 50 BP DNA, and it runs fine. I am not able to understand what is the problem. I am pasting my input .mdp parameters that I used for the run. I used semiisotropic pressure coupling as I want to keep the Z dimension of the box constant. I have also frozen 4 atoms in the 2 ends of the DNA since I want to keep the DNA aligned along Z, since I later want to apply an E field along Z direction. title = NVT equilibration with position restraint on all solute (topology modified) ; Run parameters integrator = md ; leap-frog integrator ;nsteps = 30000000 ; 1 * 500000 = 500 ps nsteps = 500000 dt = 0.001 ; 1 fs ; Output control nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstcalcenergy = 50 nstenergy = 1000 ; save energies every 1 ps nstxtcout = 2500 ;nstxout-compressed = 5000 ; save compressed coordinates every 1.0 ps ; nstxout-compressed replaces nstxtcout ;compressed-x-grps = System ; replaces xtc-grps nstlog = 1000 ; update log file every 1 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained ;lincs_iter = 2 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy epsilon_r = 15 ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cels nstlist = 10 ; 20 fs rvdw_switch = 1.0 rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = Cut-off ; Twin range cut-offs rvdw >= rlist ;vdw-modifier = Force-switch ;Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = v-rescale tc_grps = System tau_t = 1.0 ref_t = 300 ;energygrps = DNA W_ION_Protein ;energygrp-excl = DNA DNA freezegrps = DNA-Frozen-Atoms freezedim = Y Y Y ; Pressure coupling is off ;pcoupl = no ; no pressure coupling in NVT Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau_p = 5.0 compressibility = 3e-4 0 ref_p = 1.0 1.0 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correctiion DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 50 comm-mode = Linear comm-grps = System ; refcoord_scaling = com ;refcoord_scaling = all I would highly appreciate any help. Thank you in advance, Regards, Arnab Mukherjee -- 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.