Dear Gromacs users, At the moment I have some doubt on my run input .mdp file. I simulated a protein structure in water and I used parameters as following in my mdp file:
title = MD simulation of xxx ;Preprocessor cpp = /lib/cpp ;Directories to include in the topology format include = -I../top integrator = md dt = 0.001 nsteps = 1000000 nstxout = 10000 ;frequency to write velocities to output trajectory file nstvout = 10000 ;frequency to write energies to log file nstlog = 10000 ;frequency to write energies to energy file nstenergy = 10000 ;frequency to write coordinates to xtc trajectory nstxtcout = 10000 ;group(s) to write to xtc trajectory xtc_grps = prot sol XXX group(s) to write to energy file energygrps = prot sol XXX ;Frequency to update the neighbor list (and the long-range forces, ;when using twin-range cut-off's). nstlist = 10 ;Make a grid in the box and only check atoms in neighboring grid cells ;when constructing a new neighbor list every nstlist steps. ns_type = grid ;cut-off distance for the short-range neighbor list rlist = 1.4 ;treatment of electrostatic interactions coulombtype = PME fourierspacing = 0.12 pme_order = 4 rcoulomb = 1.4 ;treatment of van der waals interactions rvdw = 1.4 ; Periodic boudary conditions in all the directions pbc = xyz ;Temperature coupling tcoupl = nose-hoover tc-grps = protein NA+ CFP SOL tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 ;Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ;Velocity generation gen_vel = yes gen_temp = 300 gen_seed = 173529 ;Constrain bonds constraints = none My problem is as following: I have simulated the protein with exactly the same starting structure, the same electrostatics, the same seed for velocity generation and the same thermostating scheme three times, but I did not get exactly the same trajectory. I took the following measurement for comparing my trajectories: g_mindist -f traj.trr -s input.tpr -n index_atom1_atom2.ndx -od dist_atom1_atom2.xvg The atomic distances always differ from each other by 0.1 to 0.3 angstrom whereas the starting value at t=0 is the same. Could you tell me why I get in three different simulations with 3 totally equivalent inputs three different trajectories? In my opinion it should give 3 times a identical trajectory. Thank you in advance. Best regards, Emanuel Peter -- 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/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/mailing_lists/users.php