Hi Lara, with the .mdp you sent you are NOT going to perform a minimization, but a NPT equilibration run (i.e. a MD simulation, as stated in the first line). So check a tutorial of your choice to get a proper .mdp for a simple energy minimization.
Greetings Felix -----Ursprüngliche Nachricht----- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von Lara Bunte Gesendet: Freitag, 29. Juni 2012 12:03 An: gmx-users@gromacs.org Betreff: [gmx-users] Structure optimization failure Hello I use a CHARMM27 force field and my system is lumiflavin in water. I use the spc216 water model, a dodecahedral box with 1.3 nm. I want to make a structure minimization. I made a file pr.mdp. Could you please tell me, what I could do better in this file, or what is wrong? I guess there has to be something wrong, because GROMACS failed with grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr with the error: "Water molecule starting at atom 3924 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. " My pr.mdp file is: title = lumiflavin NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 4 ps nstvout = 5000 ; save velocities every 4 ps nstenergy = 5000 ; save energies every 4 ps nstlog = 5000 ; update log file every 4 ps ; Bond parameters continuation = yes ; Restarting after NVT 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 ; edited to 1 rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Isoalloxazin Sol ; 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 is on pcoupl = berendsen ; Pressure coupling on in 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 = all ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed Thank you for helping me Greetings Lara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
