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

[Johnny Lu]

The run was on 12 Xeon CPU with a GPU.

On Mon, Oct 6, 2014 at 3:03 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.
>>
>
>