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" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
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" <[EMAIL PROTECTED]>
> >Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]>
> >To: [EMAIL PROTECTED]
> >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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>
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>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 12 Apr 2007 10:16:39 +0200
> From: "Berk Hess" <[EMAIL PROTECTED]>
> Subject: RE: [gmx-users] wall_atomtype
> To: [EMAIL PROTECTED]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; format=flowed
>
>
>
>
> >From: Manuel Valera <[EMAIL PROTECTED]>
> >Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]>
> >To: [EMAIL PROTECTED]
> >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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>
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> End of gmx-users Digest, Vol 36, Issue 31
> *****************************************
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