[gmx-users] Re: inconsistent energy drops

[Brad Van Oosten]

This was done on v 4.6.1 

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



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