Dears,
I am trying to simulate a system of water, POPC and protein using charmm36 ff. I follow the protocol suggested in KALP15-DPPC tutorial. I follow the tutorial step by step up to NVT equilibration without any bond or any other type warnings. Then I run the grompp : # grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr My nvt.mdp file is as : define = -DPOSRES ; Parameters describing the details of the NVT simulation protocol integrator = md dt = 0.002 nsteps = 50000 ; Parameters controlling output writing nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 1000 ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz ; Parameters for treating bonded interactions continuation = no constraint_algorithm = LINCS constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Parameters for treating electrostatic interactions coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling parameters tcoupl = v-rescale tc-grps = Protein POPC SOL_CL ; Define groups to be coupled separately to temperature bath tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Pressure coupling parameters pcoupl = no ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Initial Velocity Generation gen_vel = yes gen_temp = 310 gen_seed = -1 ; Centre of mass (COM) motion removal relative to the specified groups nstcomm = 1 comm_mode = Linear comm_grps = Protein_POPC SOL_CL # mdrun -deffnm nvt -v In this step, the nvt is not done and what I get is as : Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 4707 and 4716 at distance 3.491 which is larger than the 1-4 table size 2.200 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 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 23534.929688 (between atoms 257 and 258) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 885865856.000000 (between atoms 4521 and 4520) Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 7.158197 (between atoms 3763 and 3765) 3797 3796 90.0 0.1111 0.2486 0.1111 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 11.492531 (between atoms 3712 and 3710) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4472 4469 39.4 0.1111 0.1029 0.1111 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4471 4469 89.9 0.1111 0.1222 0.1111 229 231 114.8 0.1756 169.1857 0.1430 229 230 77.2 0.1053 4.3596 0.0997 3796 3797 90.0 0.1111 0.2486 0.1111 231 251 118.0 0.1810 161.6257 0.1490 3777 3775 52.8 0.1111 0.1136 0.1111 231 232 166.9 0.1366 138.9714 0.1080 3776 3775 89.2 0.1111 0.1218 0.1111 251 252 33.6 0.1300 7.0818 0.123 and finaly some pdb files are printed. What's the problem? I checked some of atom pairs in this note, however some usual bonds are expected. Sincerely, Shima -- 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
