[gmx-users] soft-core potential in combination with PME (sorry, again)
Berk Hess
gmx3 at hotmail.com
Thu Apr 12 13:42:42 CEST 2007
I don't know about Anwars paper.
But I can say that their is no fundamental difference between PME
and RF with soft-core. With the GROMACS setup they converge
to exactly the same energies at any lambda value when you increase the RF
cut-off.
I don't understand what David Mobley meant exactly.
There is no Coulomb singularity with soft-core.
Maybe one could have an unfortunate situation where the LJ
is already very soft, but the Coulomb not very soft,
which could lead to instabilities.
But I have never encountered this.
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: RE: [gmx-users] soft-core potential in combination with PME
>(sorry,again)
>Date: Thu, 12 Apr 2007 12:38:56 +0200
>
>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.
> >
> > _________________________________________________________________
> > Hotmail en Messenger on the move http://www.msn.nl/services
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
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>posting!
> >
> > End of gmx-users Digest, Vol 36, Issue 31
> > *****************************************
>
>
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