[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

[Parvez Mh]

You should decrease the time step otherwise system will most likely explode
due to sudden increase of potential energy contribution from bond. You may
consider, dt=0.002 ps with bond constraint or dt=.001 ps with flexible bond.

--Masrul

On Wed, Mar 16, 2016 at 12:10 PM, Poncho Arvayo Zatarain <
poncho_8629 at hotmail.com> 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 potentialsrlistlong                = 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
> solvent/ionsnstcomm            = 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"
> [ system ]; NameTitle
> [ molecules ]; Compound #molsDPPC                256TIP3
> 8896
> --
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