[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

[Poncho Arvayo Zatarain]

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