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.
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
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
