Hi all, I need to do simulation which same as protein-ligand tutorial by Justin. The different is i'm using my protein and the ligand was zinc. I already follow everything in that tutorial and suddenly when i want to heat my protein by using the nvt.mdp there was an error state like below :
Fatal error: Atom 410 in multiple T-Coupling groups (1 and 2) Actually I do not understand what the error said even when i'm Google it to forum there was no one facing like mine..Here i put together my topology and the nvt.mdp. Hope you can give me some idea that i cant see. Another question,why is in the nvt.mdp at the temperature coupling there were twice of 300 of tcoupl and also the tau_t : 01. 01. Can u explain it why? topology : ; Include forcefield parameters #include "gromos53a6.ff/forcefield.itp" ; Include chain topologies #include "metal_Protein_chain_A.itp" ; Include position restraint for protein #ifdef POSRES #include "posre_Protein_chain_A.itp" #endif ; Include ion chain topologies #include "metal_Ion_chain_A2.itp" ; Include position restraint for metal #ifdef POSRES_ION #include "posre_Ion_chain_A2.itp" #endif ; Include water topology #include "gromos53a6.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "gromos53a6.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_chain_A 1 Ion_chain_A2 1 SOL 8780 NA 1 nvt.mdp : title = Protein-ligand complex NVT equilibration cpp = /usr/bin/cpp include = -I/usr/share/gromacs/top define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ZN ; Bond parameters continuation = no ; first dynamics run 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 = 10 ; 10 fs rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals 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 ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_ZN Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; 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 Thanks for your help in advance, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- 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
