[gmx-users] soft-core potential in combination with PME (sorry, again)

Thu Apr 12 12:38:56 CEST 2007

Hi Berk (and others),

Thanks a lot for your quick answer. And sorry to bother you again 
with this long email, but I still feel I'm missing something really 
essential here.

I agree that in essence the convergence and the singularity are two 
different problems. And if I understand you correctly, my first 
conclusion (that it's completely fine to use soft-core together with 
PME, that it takes care of the singularity problem, both for the VDW 
and the electrostatic part at the same time, and that it does not 
lead to additional problems) was right. So numerical instabilities 
(simulation crash) during free energy calculations resulting from 
singularities (overlapping atoms) should not be an issue with ANY 
type of electrostatics method in GROMACS (even PME), just as long as 
you use the soft-core potential.

But in that case I really don't understand why Anwar claims in his 
aforementioned paper that the electrostatics singularity problem is 
only solved by the standard soft-core potential for the simple 
truncation and reaction field schemes, and not for PME. And why David 
Mobley mentions numerical instabilities caused by "charge-charge 
overlap" (e.g. in http://www.gromacs.org/pipermail/gmx-users/2006-
March/020785.html and other mails) while using soft-core. Are the 
mentioned numerical instabilities (simulation blowing up) resulting 
from charge overlap not a direct consequence of the singularity at 
r=0? And is the soft-core potential not supposed to take care of 
exactly THIS problem, by effectively limiting the forces as r-->0? At 
least that's how I understand it from the Beutler paper and from the 
manual.

So I guess somebody is wrong here, most likely I myself, and I hope 
you or someone else can clarify this a bit further.

Thanks,
Jeroen

On Thu, 12 Apr 2007 09:19:56, Berk Hess wrote:
> Soft-core interactions are fully supported with PME.
> Both mails you quote do not state otherwise.
> 
> The second mail refers to convergence issues when
> switching off LJ as well as electrostatics interactions.
> This problem will (probably) always be present, and has
> nothing to do with the singularities in the potentials,
> but with the fact that one often has awkward free energy
> landscapes at intermediate states.
> 
> Berk.
> 
> 
> >From: "Jeroen van Bemmelen" <J.J.M.vanBemmelen at tnw.tudelft.nl>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: gmx-users at gromacs.org
> >Subject: [gmx-users] soft-core potential in combination with PME 
> >(sorry,again)
> >Date: Thu, 12 Apr 2007 01:44:41 +0200
> >
> >Hi all,
> >
> >After reading several posts on this subject on the mailing list, I'm
> >still a bit confused.
> >
> >In http://www.gromacs.org/pipermail/gmx-users/2005-
> >October/017691.html it is more or less suggested that the
> >implementation of the soft-core potential for free energy
> >calculations in combination with PME is relatively straightforward,
> >and is comparable to its implementation when using other treatments
> >of long range electrostatics. In addition, the GROMACS manual does
> >not mention any differences or problems when using this combination.
> >So from this I cautiously conclude that it's fine to use soft-core
> >together with PME, that it takes care of the singularity problem (as
> >soft-core should), and that it does not lead to additional problems
> >(at least not compared to its use with other electrostatic
> >treatments).
> >
> >However, from several discussions on this mailing list (e.g.
> >http://www.gromacs.org/pipermail/gmx-users/2006-June/022388.html) I
> >understand there are indeed problems when using this combination of
> >parameters. Not only could it lead to convergence problems (which
> >could be prevented by using a 3-stage strategy), but it could also
> >lead to stability problems because of the singularity at r=0 (for
> >which the soft-core potential was invented in the first place).
> >Moreover, reference was made to an article by Anwar (J. Chem. Phys.,
> >122, 224117 (2005)), according to which soft-core in combination with
> >PME is still a no-go (unless you use Anwars method, which is
> >significantly different from the standard GROMACS soft-core
> >implementation). So from this I conclude that the soft-core potential
> >for PME has NOT been implemented into GROMACS yet, or at least not in
> >a way that solves the singularity problem sufficiently, which is
> >contradicting my earlier conclusion.
> >
> >Obviously, I'm missing or misinterpreting something here. But could
> >someone please clear up this subject for me?
> >
> >Thanks,
> >Jeroen
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> 
> ------------------------------
> 
> Message: 8
> Date: Thu, 12 Apr 2007 10:16:39 +0200
> From: "Berk Hess" <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] wall_atomtype
> To: gmx-users at gromacs.org
> Message-ID: <BAY110-F1094B1095D1C7FECF639118E5E0 at phx.gbl>
> Content-Type: text/plain; format=flowed
> 
> 
> 
> 
> >From: Manuel Valera <valeraml at yahoo.com>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: gmx-users at gromacs.org
> >Subject: [gmx-users] wall_atomtype
> >Date: Wed, 11 Apr 2007 18:53:15 -0700 (PDT)
> >
> >Greetings to All
> >
> >I have a question about a new feature in the cvs code
> >and I was wondering if there was anybody who could
> >give
> >me a hand of a bit of help.
> >Thanks in advanced.
> >
> >I am working on a project that involves simulation of
> >confined water between two hydrophobic surfaces.
> >I noticed that recently there was an addition to the
> >gromacs source code that would allow for this kind of
> >simulations
> >
> >I downloaded the cvs source code to try out this new
> >feature, ran a small simulation of water with pbc=xy
> >and no surfaces and could see the water evaporate as
> >was expected
> >
> >The problems occurs when I need to add surfaces to the
> >
> >simulation. There are some new variables that I don't
> >know how to set and I have not been able to figure
> >this out from the source code.
> >
> >What are the appropriate values for wall_atomtype?
> >I want to have a LJ interaction between the wall and
> >the oxygen atom in
> >the water molecule.
> >How can I do this with this new feature?
> >
> >In the function do_walls we have (file wall.c)
> >
> >     if (ir->wall_type == ewt93) {
> >       fac_d[w] = ir->wall_density[w]*M_PI/6;
> >       fac_r[w] = ir->wall_density[w]*M_PI/45;
> >     } else if (ir->wall_type == ewt104) {
> >       fac_d[w] = ir->wall_density[w]*M_PI/2;
> >       fac_r[w] = ir->wall_density[w]*M_PI/5;
> >     }
> >
> >Where are these factor coming from, is there a
> >reference that I can look at?
> >
> >What would be appropriate values for the variable
> >wall_density?
> >
> >Would these be the appropriate changes to my
> >grompp.mpd file to get
> >this feature working of is there anything else that I
> >need to add?
> >
> >pbc=xy
> >nwall=2
> >wall_type=9-3
> >wall_atomtype = ? ?
> >wall_density = ? ?
> >
> >I apologized if these are too many questions!!
> >
> >I realized this a very new feature and probably it is
> >not well tested, yet I would like to try it out and
> >see if I can use this for my project
> >
> >Any help would be really appreciated.
> >
> >Thanks a lot.
> >Kind regards,
> >
> >Manuel Valera
> 
> The mdp options page of CVS:
> share/html/online/mdp_opt.html
> describes the wall mdp parameters.
> 
> wall_atomtype can be an existing atom type of the force field,
> or you can add a new atom type.
> 
> Berk.
> 
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> 
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