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

[Mark Abraham]

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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