[gmx-users] Energy conservation in NVE simulations

[Justin Lemkul]

On 12/21/16 8:57 AM, Michael K. Gilson wrote:
> Dear All,
>
> Below are more details on our efforts to maximize energy conservation in NVE
> runs with gromacs, while maintaining performance.  I'd appreciate advice on the
> following:
>
> 1) Is this level of drift about "as good as it gets"?
> 2) Or, are there ways to make it even lower?
> 3) Are there settings we can dial back to improve speed without substantially
> increasing drift?
>
> Many thanks,
> Mike Gilson
>
>    System: The system comprises 68679 waters, one protein with 6810
>    atoms, 8 sodium ions; total 75497 atoms
>
>    The input file is below. We have deliberately turned off COM
>    restraints because we are interested in how the protein moves.
>

Removal of net center-of-mass motion is not a COM restraint; your protein will 
diffuse fine with comm-mode = Linear.  The removal of net COM motion is to avoid 
the flying ice cube effect.  I suspect that failing to remove net COM motion is 
actually detrimental to conservation of energy.

-Justin

>    As noted before, for lincs-iter=4, the energy slope is approximately
>    -0.01976 kJ/mol/ps; for lincs-iter=5, the slope is approximately
>    0.00991 kJ/mol/ps. Graphs of the energy for these respective
>    conditions are provided here:
>    https://drive.google.com/open?id=0B0zEqb9pykUWRHlqSEJTa2lwYkk
>    https://drive.google.com/open?id=0B0zEqb9pykUWMWl0OEFtNGdVbzg
>
>
>
>    MDP:
>
>    ;DON'T POSITION RESTRAIN THE PROTEIN: NO -DPOSRES
>
>    ;run parameters
>    integrator      = md              ; leap-frog integrator
>    nsteps          = 10000000      ; 0.001ps * 10000000 = 10 ns
>    dt                = 0.001            ; 0.001ps smaller time step for NVE
>    comm-mode    = None       ; let center of mass move, calculate diffusion
>    constant
>
>    ; Output control
>    nstxout         = 20000          ; save coordinates every 0.5 ns
>    nstvout         = 20000          ; save velocities every 0.5 ns
>    nstenergy     = 20000         ; save energies every 0.5 ns
>    nstlog          = 20000          ; update log file every 0.5 ns
>    energygrps    = protein non-protein
>
>    ; Bond parameters
>    continuation                = yes          ; starting after nvt.mdp
>    constraint_algorithm    = lincs         ; holonomic constraints
>    constraints                 = all-bonds   ; all bonds are constrained
>    lincs_iter                    = 4             ; NVE requires high lincs-iter
>    lincs_order                 = 4             ; accuracy
>
>    ; Neighborsearching
>    cutoff-scheme           = Verlet
>    ns_type         = grid          ; search neighboring grid cells
>    nstlist           = 10            ; Frequency to update the neighbor list
>    and long range forces
>    rcoulomb              = 1.2           ; short-range electrostatic cutoff
>    (in nm)
>    rvdw                    = 1.2           ; short-range van der Waals cutoff
>    (in nm)
>    verlet-buffer-tolerance = 0.0000005    ; kJ/mol/ps per particle
>    pbc                     = xyz           ; periodic boundary conditions
>    DispCorr              = EnerPres      ; account for cut-off vdW scheme
>
>    ; Electrostatics
>    coulombtype             = PME           ; Particle Mesh Ewald for
>    long-range electrostatics
>    pme_order               = 4             ; cubic interpolation
>    fourierspacing           = 0.12          ; grid spacing for FFT
>
>
>    ; Pressure coupling is off
>    pcoupl          = no            ; fixed box size gives constant V
>
>    ; Temperature coupling is off + no simluated annealing
>    tcoupl          = no             ; NVE conditions
>
>    ; Velocity generation
>    gen_vel         = no           ; don't assign velocities: keep from
>    thermalization
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================