[gmx-users] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps
jalemkul at vt.edu
Wed Mar 16 21:41:57 CET 2016
On 3/16/16 1:10 PM, Poncho Arvayo Zatarain wrote:
> Hello. I' ḿ simulating a DPPC membrane with TIP3 water model and charmm36 forcefield and in the grompp of NVT equilibration i have this warning: (Warning 1: file topol.top line 24) The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps. Maybe you forgot to change the constraints mdp option. What can i do to solve this? I attached mu nvt.mdp and topol.top. Also i have Note 1: rlist is equal to rvdw or/and rcoulomb. There is no explicit verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be neccesari for good energy conservation.Note 2: nstcomm<nstcalcenergy defeats the purpose of nstccalenergy, setting nstcomm to nstcalcenergy
> nvt.mdptitle = NVT equilibration for DPPC-TIP3; Run parametersconstraints = h-bondscutoff-scheme = Verletintegrator = md ; leap-frog integratornsteps = 500000 ; 2 * 500000 = 1 nsdt = 1000 ; 1 ns; Output controlnstxout = 50000 ; save coordinates every 100 psnstvout = 50000 ; save velocities every 100 psnstenergy = 5000 ; save energies every 10 psnstlog = 5000 ; update log file every 10 ps; Bond parameterscontinuation = no ; first dynamics runconstraint_algorithm = lincs ; holonomic constraints lincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy; Neighborsearchingns_type = grid ; search neighboring grid celsnstlist = 10 ; 10 fsrlist = 1.4 ; short-range neighborlist cutoff (in nm)rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)rvdw = 1.2 ; short-range van der Waals cutoff (in nm)vdwtype = cutoffvdw-modifier = force-switch; long-range cut-off for switched potentialsr!
= 1.4; Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticspme_order = 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Relative dielectric constant for the medium and the reaction fieldepsilon_r = 1epsilon_rf = 1; Temperature coupling is ontcoupl = V-rescale ; modified Berendsen thermostattc-grps = DPPC TIP3 ; two coupling groups - more accuratetau_t = 0.1 0.1 ; time constant, in psref_t = 350 350 ; reference temperature, one for each group, in K; Pressure coupling is offpcoupl = no ; no pressure coupling in NVT; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correctionDispCorr = no; Velocity generationgen_vel = yes ; assign velocities from Maxwell distributiongen_temp = 350 ; temperature for Maxwell distributiongen_seed = -1 ; generate a random seed; COM motion removal; These options remove motion of the protein/bilayer relative to the solv!
tcomm = 1comm-mode = Linearcomm-grps = DPPC TIP3
> topol.top;;;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7;;;; psf2itp.py;;;; Correspondance:;; j712l362 at ku.edu or wonpil at ku.edu;;;; The main GROMACS topology file;;
> ; Include forcefield parameters#include "toppar/charmm36.itp"#include "toppar/DPPC.itp"#include "toppar/TIP3.itp"
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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