[gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures
jalemkul at vt.edu
Tue Apr 12 14:25:54 CEST 2016
On 4/11/16 4:08 PM, Rakesh Sharan wrote:
> Hi all,
> I am getting significantly different final energy during energy
How large is the difference? If it is dramatic, then your coordinates should
also be quite different and visualization should provide some clues. But given
that the water molecules are rigid, the only differences will be in nonbonded
terms, which means a different configuration. There's no guarantee that two
constraint algorithms will produce identical outcomes, though I would expect
them to be close if set up properly.
> 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:
The .mdp file is not particularly relevant, as using LINCS vs. SETTLE will have
to be done with changes to the topology file. If you're getting big differences
in outcomes, probably whatever modifications you did there are incorrect.
> 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).
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
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