[gmx-users] NVE Energy drop in Mixed Precision 4.6.7

[Johnny Lu]

here is the energy from nve1.edr
http://oi62.tinypic.com/2pqw70l.jpg

On Mon, Oct 6, 2014 at 3:01 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Hi.
>
> The system has 9000 water and a ~160 aa amino acid and uses amber99SB-ildn.
>
> After extensive NPT (300ns, 2ns ts), and then NVT equilibrium (300 ns, 2ns
> ts), the NVE simulation still has energy drop, despite of the very small
> time step.
>
> Is double precision gromacs the only solution?
>
> The mdp file is:
>
> title           = NVT equilibration
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 29500000      ; 1 ns
> dt              = 0.0002        ; 0.5 fs
>
> ;NVE
> ;nstcomm         = 500 ; remove center of mass motion to reduce energy and
> temp. drift.
> shake-tol       = 0.0000001     ; shake tolerance.
> verlet-buffer-drift = -1
>
>
> - Output control
> ;nstxout         = 20           ; save coordinates every 1.0 ps
> ;nstvout         = 4           ; save velocities every 1.0 ps
> ;nstfout                = 20
> nstenergy       = 20           ; save energies every 1.0 ps
>
> nstlog          = 1000          ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = yes           ; Restarting after NVT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 4             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 40            ; 10 fs
> rlist           = 1.3           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 6             ; cubic interpolation
> fourierspacing  = 0.1           ; grid spacing for FFT
>
> ; Temperature coupling is off
> tcoupl          = no    ; modified Berendsen thermostat
> ; Pressure coupling is off
> pcoupl          = no
>
> refcoord_scaling = com
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no            ; Velocity generation is off
> cutoff-scheme = Verlet
>
> Thank you in advance.
>