[gmx-users] Significant differences in Ewald Vs PME for clay sheet
gauravgoeluta at gmail.com
Sat Jan 24 06:48:22 CET 2015
We have used version 4.5.1.
Ewald_geometry = 3d gives exactly same results as 3dc. E.g., viral_xx is
-43303.7 in former and -43303.8 in latter.
On 23-Jan-2015 10:28 pm, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> What do you see with ewald_geometry=3d? In what GROMACS version?
> On Fri, Jan 23, 2015 at 5:47 PM, Gaurav Goel <gauravgoeluta at gmail.com>
> > A (brief) background:
> > We have prepared a periodic Na-MMT clay sheet using force-field
> > as developed by Heinz and co-workers. The box (and clay sheet) are
> > nm in x- and y- directions. Sheet thickness along z is 0.7nm and we add a
> > vacuum layer to get a box_z=4nm.
> > On using Ewald summation for electrostatic interactions, we get an exact
> > correspondence with results of Heinz et al. The equilibrium box-size in
> > 2.6nm in x and y, as reported by Heinz using Ewald summations. Further
> > Young's modulus values are in close agreement with other simulation
> > as well as experimental data.
> > However when we use PME electrostatics, we see the equilibrium box size
> > increases to 2.7nm. Also, the Young's modulus values are doubled compared
> > to Ewald summations. This prompted us to dig more into the energy and
> > values.
> > *** ***
> > As test case, we took a single snapshot of Ewald summation equilibrated
> > clay sheet configuration (box dimensions: 2.6 x 2.6 x 4 nm) and using
> > 'mdrun -rerun' determined the potential energy, forces and virial
> > components. Details are below:
> > Case 1. Ewald (fourierspacing=0.12 ~ 40 wave vectors; ewald_rtol: 1e-5;
> > rc=1.2nm)
> > Case 2: PME (fourierspacin=0.08; ewald_rtol: 1e-7; pme_order 8;
> > rc=1.2nm)
> > We have tried a few other combinations, such as standard Ewald-PME
> > of ewald_3dc, but all the numbers are same as case 2.
> > Case 1(Ewald) case 2 (PME)
> > Total PE: -404119 -404118
> > Note 1: Individual contributions to the total PE in both cases are
> > similarly matching.
> > Note 2: Force versus atom plots as obtained from .trr file is again
> > matching in the two cases.
> > However, the various Virial contributions differ significantly:
> > Vir-xx: 7444.71 -43303.8
> > Vir-yy: -6327.84 -56858.7
> > Above numbers clearly indicate a large compressive pressure in case 2
> > (PME), that is commensurate with observed increase in sheet size along x-
> > and y- directions in (semi-isotropic) NPT ensemble at zero pressure.
> > ** ** **
> > Since the virial components are determined from interparticle forces, why
> > we are seeing this difference in terms of 'force versus atom' data
> > in Ewald versus PME, but the virials showing a significant difference.
> > We will appreciate any help/suggestions on above issue. Thank you for
> > time.
> > Thanks,
> > G
> > --
> > Gaurav Goel, PhD
> > Assistant Professor
> > Department of Chemical Engineering
> > Indian Institute of Technology, Delhi
> > Hauz Khas, New Delhi 110016
> > India
> > --
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