[gmx-users] cutt offs

Tue Jan 27 21:50:01 CET 2004

It seems to me that there are no single Lennard Jones spheres that size in 
nature.  I think part of the difficulty of the doing the calculation is 
that it is inherently not physical.  Perhaps, since such a large 
Lennard-Jones sphere implies a continuum model for the material inside the 
sphere, it might be better to do a continuum model of the water as 
well.  If you did smaller spheres with explicit waters, that would be more 
physical---like a blob of methane molecules, for example.

Eric

At 10:00 PM 1/24/2004 -0800, you wrote:
>I want to calc the solvation free enenrgy of large lennard jones spheres
>with radius's of 10-15 nm. For large spheres I need to adjust the cutt off
>distance to accomidate them, which in turn stabalizes the water model, and
>increases the solvation free energy. My work around is to have two different
>cuttoff distances one for water/water and one for water/solute. I guess the
>other option is to make a cavity using smaller spheres but one sphere seems
>simpler. Do you have any other suggestons?
>
>Thanks
>
>Ilya
>
>
>-----Original Message-----
>From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
>Behalf Of Eric Jakobsson
>Sent: Tuesday, December 30, 2003 6:41 AM
>To: gmx-users at gromacs.org
>Subject: RE: [gmx-users] cutt offs
>
>
>I apologize if I seemed abrupt---I was reacting to another list-serve that
>I am on where there are lengthy debates that drown out the information.
>
>But think for a moment of the consequences of having a longer Coulomb
>cutoff for ion-water than for water-water interactions, as you
>suggested.  What you will do in that circumstance is overweigh the degree
>to which the ion polarizes the water around it, leading to systematic error
>in, for example, ion diffusion constant and solvation energy inferred from
>the calculation.
>
>Eric
>
>At 07:37 PM 12/29/2003 -0800, you wrote:
> >The reason I was asking was not to debate the subject. I am growing a LJ
> >cavity in water. When the cavity gets really big beyond the standard LJ
> >cutoff I run into problems as one might imagine. I was looking for a way to
> >overcome this problem.
> >
> >By the way. A dipole-dipole interaction falls of faster than a
>chrage-charge
> >or charge-dipole.
> >
> >Thanks for your help!!!!
> >
> >Ilya
> >
> >
> >-----Original Message-----
> >From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> >Behalf Of Eric Jakobsson
> >Sent: Monday, December 29, 2003 4:01 PM
> >To: gmx-users at gromacs.org
> >Subject: RE: [gmx-users] cutt offs
> >
> >
> >Absolutely not.
> >
> >Probably too big a gap in perception here to profitably continue such a
> >debate.
> >
> >At 01:20 PM 12/29/2003 -0800, you wrote:
> > >Your example is extreme. What about the case of a single charge in
> > >water. The water-water Coulomb cut off should be less than the charge
> > >water Coulomb cutoff.
> > >
> > >Ilya
> > >
> > >
> > >-----Original Message-----
> > >From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
> > >On Behalf Of David van der Spoel
> > >Sent: Monday, December 29, 2003 12:40 PM
> > >To: gmx-users at gromacs.org
> > >Subject: RE: [gmx-users] cutt offs
> > >
> > >On Mon, 29 Dec 2003, Ilya Chorny wrote:
> > >
> > > >Its not obvious to me why the thermodynamics would get screwed up. Its
> > > >intuitively the same as having different cut offs for LJ vs Coul.
> > >That is an approximation, and since LJ potential goes to zero faster it
> > >can be justified (although that does not mean it is correct).
> > >Treating different parts of the system with different
> > >cut-off is worse. Let's say we divided a 6x6x6 nm system in two pieces,
> > >that with X coordinate < 3 nm and that with X > 3 nm. Now if we use a
> > >different cut-off for the first half of the system than for the other
> > >half, we create artifacts on the border between the two, and what's
> > >more,
> > >I suspect that for such a system in "equilibrium" the chemical potential
> > >
> > >is not the same in both halves. It will hence be impossible to define
> > >what
> > >kind of ensemble is modeled. Treating cut-offs differently for the
> > >protein
> > >and water is the same kind of division, comparable in nature to
> > >simulations in implicit solvent.
> > >
> > > >
> > > >>You would not want to do that anyway--it would really put you in
> > > >>thermodynamic neverland.
> > > >I agree, but IIRC this is what Amber does quite frequently, no cut-off
> > > >within the protein, and short cut-off for protein-water and water-water
> > >
> > > >(e.g. the 1 us folding sim of Duan and Kollman).
> > >
> > >And to come back to that simulation, they also determined solvation free
> > >
> > >energies from that, but from just the protein coordinates, dismiising
> > >all the
> > >solvent.
> > >
> > >Just my (possibly biased) opinion...
> > >
> > >--
> > >David.
> > >________________________________________________________________________
> > >David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > >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://xray.bmc.uu.se/~spoel
> > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
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> >---------------------------------
> >Eric Jakobsson, Ph.D.
> >Professor, Department of Molecular and Integrative Physiology, and of
> >Biochemistry
> >Senior Research Scientist, National Center for Supercomputing Applications
> >Professor, Beckman Institute for Advanced Science and Technology
> >4021 Beckman Institute, mc251
> >405 N. Mathews Avenue
> >University of Illinois, Urbana, IL 61801
> >ph. 217-244-2896       fax 217-244-2909
> >
> >(Currently on leave to NIH to serve as Director of Center for
> >Bioinformatics and Computational Biology at the National Institute of
> >General Medical Sciences and Chair of the NIH Biomedical Information
> >Science and Technology Initiative Consortium.  Usual schedule is four days
> >a week at NIH and three days a week at Illlinois.)
> >
> >
> >
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>---------------------------------
>Eric Jakobsson, Ph.D.
>Professor, Department of Molecular and Integrative Physiology, and of
>Biochemistry
>Senior Research Scientist, National Center for Supercomputing Applications
>Professor, Beckman Institute for Advanced Science and Technology
>4021 Beckman Institute, mc251
>405 N. Mathews Avenue
>University of Illinois, Urbana, IL 61801
>ph. 217-244-2896       fax 217-244-2909
>
>(Currently on leave to NIH to serve as Director of Center for
>Bioinformatics and Computational Biology at the National Institute of
>General Medical Sciences and Chair of the NIH Biomedical Information
>Science and Technology Initiative Consortium.  Usual schedule is four days
>a week at NIH and three days a week at Illlinois.)
>
>
>
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

(Currently on leave to NIH to serve as Director of Center for 
Bioinformatics and Computational Biology at the National Institute of 
General Medical Sciences and Chair of the NIH Biomedical Information 
Science and Technology Initiative Consortium.  Usual schedule is four days 
a week at NIH and three days a week at Illlinois.)