[gmx-developers] RE: modifing nonbonded interactions
Jim Kress
ccl_nospam at kressworks.com
Sat Oct 25 17:08:42 CEST 2008
Why don't you use a lumped model of water and take advantage of a more
mesoscopic approach like the ones incorporated in gromacs?
Jim
> -----Original Message-----
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> Today's Topics:
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> 1. RE: modifing nonbonded interactions (Nazish Hoda)
> 2. Re: modifing nonbonded interactions (Mark Abraham)
> 3. RE: modifing nonbonded interactions (Nazish Hoda)
> 4. Re: modifing nonbonded interactions (David van der Spoel)
> 5. Re: modifing nonbonded interactions (Mark Abraham)
> 6. Re: modifing nonbonded interactions (Berk Hess)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 23 Oct 2008 21:41:34 -0400
> From: "Nazish Hoda" <nazish at umich.edu>
> Subject: RE: [gmx-developers] modifing nonbonded interactions
> To: "'Discussion list for GROMACS development'"
> <gmx-developers at gromacs.org>
> Message-ID: <000001c93579$ab220c20$01662460$@edu>
> Content-Type: text/plain; charset="us-ascii"
>
> To do implicit-water md for a charged system. In the
> explicit-water md, water is non-uniformly distributed along
> the molecules. I am trying to incorporate this effect in my
> implicit-water simulation.
>
> -Nazish
>
> -----Original Message-----
> From: gmx-developers-bounces at gromacs.org
> [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of Mark Abraham
> Sent: Thursday, October 23, 2008 9:04 PM
> To: Discussion list for GROMACS development
> Subject: Re: [gmx-developers] modifing nonbonded interactions
>
> Nazish Hoda wrote:
> > This is what I am thinking. I know it is an approximation,
> but I don't
> know
> > how bad would this be.
> > Let me know what you people think.
> > In PME,
> > E_coul = E_coul^SR + E_coul^LR. (and the same holds for force)
> >
> > My cut off for dielectric permittivity, which I call r_1, is very
> > small,
> and
> > would
> > only affect E_coul^SR (F_coul^SR). So what I think is that just
> > changing E_coul^SR (F_coul^SR) might work.
>
> Sure, subject to the foregoing force discontinuity issues,
> but what purpose might this serve? IIRC the purpose of a
> distance-dependent dielectric is to model heuristically
> either an effective dielectric constant, or one that allows
> the Coulomb sum to converge faster, or both. Since under PME
> the convergence of the short-range sum is already rapid, and
> common water models like SPC and TIPxP are parameterized for
> the use of a constant dielectric, you'd have many stones to
> roll up the hill to possibly get an inconclusive result.
>
> Mark
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>
> ------------------------------
>
> Message: 2
> Date: Fri, 24 Oct 2008 12:44:52 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-developers] modifing nonbonded interactions
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <49012894.3090901 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Nazish Hoda wrote:
> > To do implicit-water md for a charged system. In the
> explicit-water md,
> > water is
> > non-uniformly distributed along the molecules. I am trying
> to incorporate
> > this
> > effect in my implicit-water simulation.
>
> PME requires periodicity, which you shouldn't need for implicit-water.
>
> If you're really wanting to do implicit-water simulation, you
> should be
> looking at simulation packages other than GROMACS.
>
> Mark
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 23 Oct 2008 22:01:42 -0400
> From: "Nazish Hoda" <nazish at umich.edu>
> Subject: RE: [gmx-developers] modifing nonbonded interactions
> To: "'Discussion list for GROMACS development'"
> <gmx-developers at gromacs.org>
> Message-ID: <000101c9357c$7657eb60$6307c220$@edu>
> Content-Type: text/plain; charset="us-ascii"
>
> > PME requires periodicity, which you shouldn't need for
> implicit-water.
> There are still charged molecules in the neighboring, next
> neighboring, etc
> boxes.
> How to account for them ?
>
> >If you're really wanting to do implicit-water simulation,
> you should be
> >looking at simulation packages other than GROMACS.
>
> Won't using a modified LJ parameters work ?
>
> Nazish
>
> -----Original Message-----
> From: gmx-developers-bounces at gromacs.org
> [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of Mark Abraham
> Sent: Thursday, October 23, 2008 9:45 PM
> To: Discussion list for GROMACS development
> Subject: Re: [gmx-developers] modifing nonbonded interactions
>
> Nazish Hoda wrote:
> > To do implicit-water md for a charged system. In the
> explicit-water md,
> > water is
> > non-uniformly distributed along the molecules. I am trying
> to incorporate
> > this
> > effect in my implicit-water simulation.
>
> PME requires periodicity, which you shouldn't need for implicit-water.
>
> If you're really wanting to do implicit-water simulation, you
> should be
> looking at simulation packages other than GROMACS.
>
> Mark
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
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>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 24 Oct 2008 06:17:07 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-developers] modifing nonbonded interactions
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <49014C43.1030201 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Mark Abraham wrote:
> > Nazish Hoda wrote:
> >> To do implicit-water md for a charged system. In the
> explicit-water md,
> >> water is non-uniformly distributed along the molecules. I
> am trying to
> >> incorporate
> >> this effect in my implicit-water simulation.
>
> Author(s): Hess B, Holm C, van der Vegt N
> Source: PHYSICAL REVIEW LETTERS Volume: 96 Issue: 14 Article
> Number: 147801 Published: APR 14 2006
> Times Cited: 9 References: 19 Citation MapCitation Map beta
> Abstract: We report a new strategy to parametrize effective ion-ion
> potentials for implicit solvent simulations of charged systems. The
> effective potential includes a pair term and a Coulomb term that by
> means of a concentration dependent dielectric permittivity takes into
> account multibody effects. We demonstrate that this approach
> allows us
> to accurately reproduce the solution osmotic properties and the ion
> coordination up to concentrations of 2.8 M aqueous NaCl.
>
> >
> > PME requires periodicity, which you shouldn't need for
> implicit-water.
> >
> > If you're really wanting to do implicit-water simulation,
> you should be
> > looking at simulation packages other than GROMACS.
> >
> > Mark
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-developers-request at gromacs.org.
>
>
> --
> David.
> ______________________________________________________________
> __________
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 24 Oct 2008 15:17:51 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-developers] modifing nonbonded interactions
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <49014C6F.4090005 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Nazish Hoda wrote:
> >> PME requires periodicity, which you shouldn't need for
> implicit-water.
> > There are still charged molecules in the neighboring, next
> neighboring, etc
> > boxes.
> > How to account for them ?
>
> If your system has a net charge, you have even more problems if you
> require no solvent (so no counter-ions) and periodicity. PME doesn't
> work for systems with net non-zero charge.
>
> >> If you're really wanting to do implicit-water simulation,
> you should be
> >> looking at simulation packages other than GROMACS.
> >
> > Won't using a modified LJ parameters work ?
>
> Life is not that simple. These parameters are carefully optimized to
> reproduce some (often vaguely) relevant data. It's inconceivable that
> any form of 6,12 potential on solute atoms could account for the
> electrostatic, frictional, thermostatic, dispersion and
> doubtless other
> effects that explicit solvents have upon their solutes. See
> http://wiki.gromacs.org/index.php/Parameterization
>
> Mark
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 24 Oct 2008 09:44:41 +0200
> From: Berk Hess <hessb at mpip-mainz.mpg.de>
> Subject: Re: [gmx-developers] modifing nonbonded interactions
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <49017CE9.50806 at mpip-mainz.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
>
> To understand the approximations, lets have a look at the
> simplest case:
> two single-atomic ions in water.
>
> In general the dielectric permittivity of the medium around a
> single ion is:
> (1) eps(r)
> When you have two ions this I already don't see a reasonable
> approximation
> to describe the permittivity, but lets say for arguments sake
> that it is
> still (1).
> (If you read my papers you will see that even for high
> concentrations of
> NaCl(aq)
> the permittivity still seems near to constant of the whole space,
> surprisingly this
> even seems to hold for an Na-Cl contact pair!).
>
> For two ions one can DEFINE the electrostatic interaction as:
> (2) c(r)/r
> Note that c(r) is NOT equal to 1/eps(r). To get c(r) from
> eps(r) you have
> to solve the electrostatics problem with spatially varying
> permittivity.
>
> For multi-atomic ions/molecules it is not clear how good
> approximation
> (1) is.
> For systems with more than two molecules (2) will be a (maybe bad)
> approximation.
> But using (2) in Gromacs with PME is possible, if c(r) is a constant
> eps1 after the cut-off.
> Then you should use:
> coulomb_type = pme-user
> epsilon_r = eps1
> and fill the Coulomb table with eps1*c(r)/r.
>
> But as Mark said, the real work will be in parameterizing the "LJ"
> interactions,
> which are no longer simply LJ, but contain all kinds of
> multi-body effects.
>
> I think it would be much simpler and also not such a bad approximation
> (especially compared to the many other approximations) to
> assume that the
> permittivity is constant over space.
>
> PS: Many people on this list seem to think that you do not
> need periodicity
> with implicit solvent. This is only true when you have a
> single molecule
> or a complex. In many cases, such as aggregation studies, one needs
> periodic boundary conditions.
>
> Berk
>
>
> Mark Abraham wrote:
> > Nazish Hoda wrote:
> >>> PME requires periodicity, which you shouldn't need for
> implicit-water.
> >> There are still charged molecules in the neighboring, next
> >> neighboring, etc
> >> boxes.
> >> How to account for them ?
> >
> > If your system has a net charge, you have even more problems if you
> > require no solvent (so no counter-ions) and periodicity.
> PME doesn't
> > work for systems with net non-zero charge.
> >
> >>> If you're really wanting to do implicit-water simulation,
> you should
> >>> be looking at simulation packages other than GROMACS.
> >>
> >> Won't using a modified LJ parameters work ?
> >
> > Life is not that simple. These parameters are carefully
> optimized to
> > reproduce some (often vaguely) relevant data. It's
> inconceivable that
> > any form of 6,12 potential on solute atoms could account for the
> > electrostatic, frictional, thermostatic, dispersion and doubtless
> > other effects that explicit solvents have upon their solutes. See
> > http://wiki.gromacs.org/index.php/Parameterization
> >
> > Mark
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-developers-request at gromacs.org.
>
>
>
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