AW: [gmx-users] Structure optimization failure
frausch at ipb-halle.de
Fri Jun 29 12:26:14 CEST 2012
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.
Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Im Auftrag von Lara Bunte
Gesendet: Freitag, 29. Juni 2012 12:03
An: gmx-users at gromacs.org
Betreff: [gmx-users] Structure optimization failure
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
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)
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
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