[gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures

Rakesh Sharan rs11chembhu at gmail.com
Mon Apr 11 22:09:00 CEST 2016

Hi all,

I am getting significantly different final energy during energy
minimization of a box of bulk TIP4P/2005 water using SETTLE and LINCS as
constraint algorithms. I do not know which is more reliable in the sense
that which one is giving correct converged configurations starting from the
same initial configuration.

I would highly appreciate your comments/suggestions over this discrepancy.

The mdp file that I am using is following:

integrator              = steep         ; steepest descents energy
nsteps                  = 10000          ; maximum number of steps to

emtol                   = 1.0          ; [kJ/mol/nm] minimization is
converged when max force is < emtol
emstep                  = 0.01          ; [nm] initial step-size

nstxtcout               = 10            ; [steps] freq to write to
coordinate file
nstlog                  = 10            ; [steps] freq to write energies to
log file
nstenergy               = 10            ; [steps] freq to write energies to
energy file
xtc_grps                = System        ; coordinate group(s) to write to
energygrps              = System        ; group(s) to write to energy file

nstlist                 = 1             ; [steps] freq to update neighbor
ns_type                 = grid          ; method of updating neighbor list
pbc                     = xyz           ; periodic boundary conditions in
all directions
rlist                   = 0.95           ; [nm] cut-off distance for the
short-range neighbor list

rcoulomb                = 0.95          ; [nm] distance for Coulomb cut-off

vdw-type                = cut-off       ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw                    = 0.95          ; [nm] distance for LJ cut-off
DispCorr                = Ener          ; apply long range dispersion
corrections for energy

;constraints            = none
coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
pme_order               = 4             ; interpolation order for PME, 4 =
fourierspacing          = 0.12



Rakesh S. Singh, Ph.D.
Postdoctoral Research Associate,
Department of Chemical & Biological Engineering,
Princeton University,
Princeton, NJ 08544 (US).

More information about the gromacs.org_gmx-users mailing list