[gmx-developers] Implementation of fluctuating charge into GROMACS: Pressure calculation
David van der Spoel
spoel at xray.bmc.uu.se
Sat Oct 16 22:25:33 CEST 2010
On 2010-10-16 22.16, Lee-Ping Wang wrote:
> Hi there,
> I’ve gotten the QTPIE interaction to work with PBC using a
> custom-designed shift function; the matrix elements are taken smoothly
> to zero at the cutoff radius. This ensures that there is no force
> discontinuity, which I’ve found causes some artifacts in the dynamics
> and energy minimization.
> Implementing the Ewald summation has been a bit problematic, because as
> you said, there needs to be a pairwise decomposition of the
> electrostatic energy in computing the matrix elements. I think I have
> something that works, but the forces aren’t implemented yet, and it’s
> expensive because it requires a double loop in the k-space summation
> (the normal Ewald summation only needs a single loop). Hopefully, the
> shift function will perform well enough and I won’t worry so much about
> the Ewald summation.
> I am trying to build the QTPIE forces into the “fshift” vector to get
> the pressures right, but I don’t have any way of telling whether my
> calculated pressures are correct. I suspect there is a problem, since
> the box keeps on blowing up if I turn pressure coupling on, but I need
> some reference method to compare against; how do you all make sure that
> the pressure is being computed properly? Do you simply repeat energy
> calculations at different box sizes and compute the pressure by finite
You can run NVT and monitor the pressure for one thing. But the way to
go is to put something really simple in a box, e.g. two water molecules,
such that you can test your implementation analytically.
> - Lee-Ping
> *From:* gmx-developers-bounces at gromacs.org
> [mailto:gmx-developers-bounces at gromacs.org] *On Behalf Of *Gerrit Groenhof
> *Sent:* Wednesday, October 13, 2010 2:34 AM
> *To:* Discussion list for GROMACS development
> *Subject:* Re: [gmx-developers] rlist larger than L/2 in simple neighbor
> On 10/12/2010 06:49 PM, Lee-Ping Wang wrote:
> Hi there,
> For the past few months, I’ve been adding a charge equilibration model
> to GROMACS (to be specific, QTPIE – a refinement of QEq). For the model
> to work properly, each atom must “see” each other atom in the
> electrostatic interaction (it is a screened Coulomb interaction). This
> is easy enough to do with pbc = no; I just set all the cutoffs to zero,
> and add a new neighbor-list that includes excluded atom pairs.
> Since we'd be interested in that, I would appreciate if you can keep us
> informed of your progress.
> Now I would like to run the simulation with PBC turned on, which means
> either implementing Ewald summation or using cutoffs for the
> electrostatic interaction. When cutoffs are turned on (with or without
> PBC), the model goes haywire even with very long cutoff lengths. I
> haven’t implemented Ewald summation for the screened Coulomb
> interaction, and I’m not sure if it’s worth the effort if an easier fix
> is possible.
> If I recall correctly, the screened Coulomb here means the overlap
> integral between s-type Slater functions. This interaction behave as a
> normal coulomb at large distances, so that coudl explain the issues with
> increasing the cut-off. But an Ewald expression will be difficult as
> well, since the all pairs-wise interactions are required to compute the
> charge flow parameters. I have so far only seen it applied to molecules.
> For non bonded system like a box of water, a direct charge flow between
> atoms far apart is unlikely though. Could one not simply scale also the
> charge transfer variables to zero with distance as well?
> As a quick fix, I changed the simple neighbor-searching code to set rcut
> = 1000000 when QTPIE is turned on.
> I am worried about the other possible consequences of my change; will
> this adversely affect the molecular dynamics or create artifacts in some
> unexpected way?
> You will get the ordinary artefacts caused by cutoff, like ordering etc.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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