[gmx-users] Re: inconsistent energy drops

[Justin Lemkul]

On 8/1/13 5:08 PM, Brad Van Oosten wrote:
> This was done on v 4.6.1
>

Does the same problem persist in 4.6.3?

-Justin

> md50.mdp:
>
>
> title			 = MD simulation
> integrator               = md			; MD integrator
> tinit                    = 0
> dt                       = 0.002		; 2 fs timestep
> nsteps                   = 50000000		; Number of steps
> pbc			 = xyz			; Periodic boundary conditions in xyz
> comm-mode                = linear			
> nstcomm                  = 1
> comm-grps                = SOL_CL DMPC_CCCHX		
>
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 0			; Do not want .trr-files
> nstxtcout                = 1000			; But do want .xtc-files
> nstvout                  = 0			; No velocities in output
> nstfout                  = 0			; No forces in output
> nstlist			 = 20			; Update neighbor list between cut-offs
> ns_type			 = grid			; Fastest option
> nstenergy		 = 1000			; .edr-file output
> energygrps		 = DMPC_CCCHX SOL_CL		; Energy groups
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> cutoff-scheme = Verlet
> coulombtype              = pme			; Particle mesh Ewald, do not change
> rcoulomb                 = 1.4			; Real-space cut-off
>
> rlist			 = 1.0			; Short-range neighbor list
> rlistlong		 = 1.6			; Long-range neighbor list
> rvdw                     = 1.4			
> DispCorr                 = EnerPres		; Dispersion corrections to both the
> potential and pressure
> table-extension          = 1
> fourierspacing		 = 0.12			; PME grid
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> tcoupl                   = nose-hoover		; Thermostat, v-rescale is also fine
> tc-grps                  = DMPC_CCCHX SOL_CL		; Couple lipids and SOL
> seperatly
> tau-t                    = 1.0 1.0		; Time constant for temperature coupling
> ref-t                    = 323 323		; Desired temperature (K)
> Pcoupl                   = parrinello-rahman	; Barostat
> Pcoupltype               = semiisotropic	; Pressure in xy and z couple
> separately
> ref-p                    = 1.013 1.013		; Desired pressure (bar)
> tau-p                    = 10.0 10.0		; Time constant for pressure coupling
> compressibility          = 4.5e-5 4.5e-5	; Same as for water
>
> ; CONSTRAINTS
> constraints              = all-bonds		; Constrain all bonds
> constraint-algorithm     = Lincs		; With Lincs
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/inconsistent-energy-drops-tp5010260p5010297.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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