Hi, I think the problem is epsilon_r=80, which reduces your electrostatics interactions by a factor of 80.
Berk > Date: Mon, 13 Dec 2010 17:46:14 -0500 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] pathologically expanding box > > > > Greg Bowman wrote: > > Hello, > > > > Has anyone else experienced a pathologically expanding box during > > equilibration in the NPT ensemble? I've solvated my system with > > editconf/genbox, energy minimized, equilibrated in NVT with the protein > > coordinates restrained, and then equilibrated in NPT without any > > position restraints. During the NPT equilibration all the box > > dimensions are doubling and the density decreases drastically. > > > > I'm using the v-rescale thermostat and the Berendsen barostat in gromacs > > 4.5.3 with the AMBER03 force field and tip3p water. I've also tried > > OPLSAA with SPC water, a number of different box types (cubic, > > octahedral, dodecahedral), and shorter tau_t and tau_p settings. I also > > tried adding another energy minimzation step between my NVT and NPT phases. > > > > Is the temperature, potential energy, etc. stable after NVT? > > Is the increase in box size steady, oscillating, or sudden? > > Does the problem persist with different combinations of thermostat and > barostat, > or is it limited to V-rescale + Berendsen? > > -Justin > > > My mdp settings for the NPT ensemble are below. > > > > Thanks for your help. > > > > Greg > > > > ; RUN CONTROL PARAMETERS > > ;define = -DPOSRES > > integrator = md > > tinit = 0 > > nsteps = 50000 > > dt = 0.002000 > > comm-mode = linear > > nstcomm = 4 > > > > ; CONSTRAINTS > > constraints = all-bonds > > lincs_order = 6 > > lincs_iter = 2 > > > > ; NEIGHBORSEARCHING PARAMETERS > > ns_type = grid > > nstlist = 4 > > rlist = 1.2 > > pbc = xyz > > > > ; ELECTROSTATICS > > coulombtype = pme ;-switch > > rcoulomb = 1.2 > > ;rcoulomb-switch = 0.800000 > > fourierspacing = 0.120000 > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > pme_order = 6 > > ewald_rtol = 0.000001 > > ewald_geometry = 3d > > epsilon_surface = 0 > > optimize_fft = yes > > epsilon_r = 80 > > > > ; VDW > > vdw-type = switch > > rvdw = 1.2 > > rvdw-switch = 1.1 > > DispCorr = EnerPres > > > > ; OUTPUT CONTROL OPTIONS > > ; Output frequency for coords (x), velocities (v) and forces (f) = > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > nstlog = 0 > > energygrps = System > > nstenergy = 100 > > nstcalcenergy = 1 > > nstxtcout = 0 > > xtc-grps = Protein > > > > Tcoupl = v-rescale > > tau_t = 0.5 > > tc-grps = System > > ref_t = 300 > > ld_seed = -1 > > > > Pcoupl = berendsen > > Pcoupltype = isotropic > > tau_p = 5 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > > > gen_vel = yes > > gen_temp = 300.0 > > gen_seed = -1 > > > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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