[gmx-developers] RE: modifing nonbonded interactions

Nazish Hoda nazish at umich.edu
Sat Oct 25 18:26:20 CEST 2008


Do you mean Brownian/Stochastic dynamics simulations or something else?

Nazish

-----Original Message-----
From: gmx-developers-bounces at gromacs.org
[mailto:gmx-developers-bounces at gromacs.org] On Behalf Of Jim Kress
Sent: Saturday, October 25, 2008 11:09 AM
To: gmx-developers at gromacs.org
Subject: [gmx-developers] RE: modifing nonbonded interactions 

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-----
> From: gmx-developers-bounces at gromacs.org 
> [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of 
> gmx-developers-request at gromacs.org
> Sent: Friday, October 24, 2008 6:00 AM
> To: gmx-developers at gromacs.org
> Subject: gmx-developers Digest, Vol 54, Issue 24
> 
> Send gmx-developers mailing list submissions to
> 	gmx-developers at gromacs.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.gromacs.org/mailman/listinfo/gmx-developers
> or, via email, send a message with subject or body 'help' to
> 	gmx-developers-request at gromacs.org
> 
> You can reach the person managing the list at
> 	gmx-developers-owner at gromacs.org
> 
> When replying, please edit your Subject line so it is more 
> specific than "Re: Contents of gmx-developers digest..."
> 
> 
> Today's Topics:
> 
>    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
> _______________________________________________
> 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.
> 
> 
> 
> 
> 
> ------------------------------
> 
> 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
> 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.
> 
> 
> 
> 
> 
> ------------------------------
> 
> 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.
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> 
> 
> End of gmx-developers Digest, Vol 54, Issue 24
> **********************************************

_______________________________________________
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.






More information about the gromacs.org_gmx-developers mailing list