Hi Thank you for the fast answer :-) I use a tip3p water model. I wrote spc216 because this is what I am using with genbox. My mistake.
Now I used the equilibrating file out of this tutorial: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html I got the same problem. The water could not be settled. What is wrong with this file for my system? Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Lara Bunte <lara.bu...@yahoo.de>; Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 12:23 Freitag, 29.Juni 2012 Betreff: Re: [gmx-users] Structure optimization failure On 6/29/12 6:01 AM, Lara Bunte wrote: > 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 CHARMM27 should be combined with TIP3P, not SPC. > 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: > Your problem is that you're trying to run position-restrained MD, not energy minimization. Consult any tutorial for a more appropriate EM file. Without adequate EM, any simulation with almost certainly crash. -Justin > > 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 > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
