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

[Mark Abraham]

Hi,

For what absolute value of energy was the force field parameterized?

Mark

On Fri, Oct 10, 2014 at 7:38 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Well... at that rate, after I run 100 ns, the energy will decrease by 100%.
>
> On Tue, Oct 7, 2014 at 8:27 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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