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

[Mark Abraham]

Sure, there's drift. But is it significant? What is its value in units of
k_B T / dof / ns? How much will such drift affect the quality of your
observables? Is that more significant than your other approximations (force
field parameterization targets not matching your observables, no
polarization, incomplete sampling, lack of replicates)? Is fixing it worth
the hit of more than a factor of two in number of samples?

It's relatively easy to feel good about solving the one problem that you
can solve. But only solve it if it's the one that matters ;-)

Mark

On Mon, Oct 6, 2014 at 9:03 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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.
> >
> --
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