[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

[Justin Lemkul]

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!
 listlong  
              = 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!
 ent/ionsns
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"

Please make an effort to make your emails readable by using sensible line 
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-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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