[gmx-users] Significant differences in Ewald Vs PME for clay sheet

[Mark Abraham]

On Sat, Jan 24, 2015 at 6:48 AM, Gaurav Goel <gauravgoeluta at gmail.com>
wrote:

> Hi mark,
>
> 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.
>

OK, thanks. In practice, probably only Berk has any clue what this code
does and how, and if there's a problem then we'd need to know whether it
still exists in the latest versions (e.g. 5.0.4). Can you try that on your
inputs, please?

Mark


> Regards,
> G
>  On 23-Jan-2015 10:28 pm, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>
> > Hi,
> >
> > What do you see with ewald_geometry=3d? In what GROMACS version?
> >
> > Mark
> >
> > On Fri, Jan 23, 2015 at 5:47 PM, Gaurav Goel <gauravgoeluta at gmail.com>
> > wrote:
> >
> > > A (brief) background:
> > >
> > > We have prepared a periodic Na-MMT clay sheet using force-field
> > parameters
> > > as developed by Heinz and co-workers. The box (and clay sheet) are
> > 2.6-2.7
> > > 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
> > the
> > > Young's modulus values are in close agreement with other simulation
> > studies
> > > 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
> > force
> > > 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;
> > ewald_3dc;
> > > rc=1.2nm)
> > > We have tried a few other combinations, such as standard Ewald-PME
> > instead
> > > 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
> > exactly
> > > 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
> > matching
> > > in Ewald versus PME, but the virials showing a significant difference.
> > >
> > > We will appreciate any help/suggestions on above issue. Thank you for
> > your
> > > 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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