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Hi,<br><br>I think the problem is epsilon_r=80, which reduces your electrostatics interactions<br>by a factor of 80.<br><br>Berk<br><br>> Date: Mon, 13 Dec 2010 17:46:14 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] pathologically expanding box<br>> <br>> <br>> <br>> Greg Bowman wrote:<br>> > Hello,<br>> > <br>> > Has anyone else experienced a pathologically expanding box during <br>> > equilibration in the NPT ensemble? I've solvated my system with <br>> > editconf/genbox, energy minimized, equilibrated in NVT with the protein <br>> > coordinates restrained, and then equilibrated in NPT without any <br>> > position restraints. During the NPT equilibration all the box <br>> > dimensions are doubling and the density decreases drastically.<br>> > <br>> > I'm using the v-rescale thermostat and the Berendsen barostat in gromacs <br>> > 4.5.3 with the AMBER03 force field and tip3p water. I've also tried <br>> > OPLSAA with SPC water, a number of different box types (cubic, <br>> > octahedral, dodecahedral), and shorter tau_t and tau_p settings. I also <br>> > tried adding another energy minimzation step between my NVT and NPT phases.<br>> > <br>> <br>> Is the temperature, potential energy, etc. stable after NVT?<br>> <br>> Is the increase in box size steady, oscillating, or sudden?<br>> <br>> Does the problem persist with different combinations of thermostat and barostat, <br>> or is it limited to V-rescale + Berendsen?<br>> <br>> -Justin<br>> <br>> > My mdp settings for the NPT ensemble are below.<br>> > <br>> > Thanks for your help.<br>> > <br>> > Greg<br>> > <br>> > ; RUN CONTROL PARAMETERS<br>> > ;define = -DPOSRES<br>> > integrator = md<br>> > tinit = 0<br>> > nsteps = 50000<br>> > dt = 0.002000<br>> > comm-mode = linear<br>> > nstcomm = 4<br>> > <br>> > ; CONSTRAINTS<br>> > constraints = all-bonds<br>> > lincs_order = 6<br>> > lincs_iter = 2<br>> > <br>> > ; NEIGHBORSEARCHING PARAMETERS<br>> > ns_type = grid<br>> > nstlist = 4<br>> > rlist = 1.2<br>> > pbc = xyz<br>> > <br>> > ; ELECTROSTATICS<br>> > coulombtype = pme ;-switch<br>> > rcoulomb = 1.2<br>> > ;rcoulomb-switch = 0.800000<br>> > fourierspacing = 0.120000<br>> > fourier_nx = 0<br>> > fourier_ny = 0<br>> > fourier_nz = 0<br>> > pme_order = 6<br>> > ewald_rtol = 0.000001<br>> > ewald_geometry = 3d<br>> > epsilon_surface = 0<br>> > optimize_fft = yes<br>> > epsilon_r = 80<br>> > <br>> > ; VDW<br>> > vdw-type = switch<br>> > rvdw = 1.2<br>> > rvdw-switch = 1.1<br>> > DispCorr = EnerPres<br>> > <br>> > ; OUTPUT CONTROL OPTIONS<br>> > ; Output frequency for coords (x), velocities (v) and forces (f) =<br>> > nstxout = 0<br>> > nstvout = 0<br>> > nstfout = 0<br>> > nstlog = 0<br>> > energygrps = System<br>> > nstenergy = 100<br>> > nstcalcenergy = 1<br>> > nstxtcout = 0<br>> > xtc-grps = Protein<br>> > <br>> > Tcoupl = v-rescale<br>> > tau_t = 0.5<br>> > tc-grps = System<br>> > ref_t = 300<br>> > ld_seed = -1<br>> > <br>> > Pcoupl = berendsen<br>> > Pcoupltype = isotropic<br>> > tau_p = 5<br>> > compressibility = 4.5e-5<br>> > ref_p = 1.0<br>> > <br>> > gen_vel = yes<br>> > gen_temp = 300.0<br>> > gen_seed = -1<br>> > <br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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