[gmx-users] cutt offs
David
spoel at xray.bmc.uu.se
Tue Jan 27 22:06:01 CET 2004
On Tue, 2004-01-27 at 21:48, Eric Jakobsson wrote:
> 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.
>
One of the beauties of the MD algorithm is that you can use it for
non-physical or just plain weird things. I think weather prediction by
MD will be vastly superior to the current crap...
Further, I think the request is not unreasonable, as it is this division
that (I have heard) was used by Kollman in his famous microsecond sim.
of Villin. No cut-off within the protein, but protein-water and
water-water was at 8Å. Of course that can be debated as well...
Nevertheless, this is not implemented now. It would require hacking of
the neighbour searching. Basically, define a matrix of cut-offs with the
energy-group number as an index.
> 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
> > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > >
> > > >_______________________________________________
> > > >gmx-users mailing list
> > > >gmx-users at gromacs.org
> > > >http://www.gromacs.org/mailman/listinfo/gmx-users
> > > >Please don't post (un)subscribe requests to the list. Use the
> > > >www interface or send it to gmx-users-request at gromacs.org.
> > > >
> > > >
> > > >_______________________________________________
> > > >gmx-users mailing list
> > > >gmx-users at gromacs.org
> > > >http://www.gromacs.org/mailman/listinfo/gmx-users
> > > >Please don't post (un)subscribe requests to the list. Use the
> > > >www interface or send it to gmx-users-request at gromacs.org.
> > >
> > >---------------------------------
> > >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.)
> > >
> > >
> > >
> > >_______________________________________________
> > >gmx-users mailing list
> > >gmx-users at gromacs.org
> > >http://www.gromacs.org/mailman/listinfo/gmx-users
> > >Please don't post (un)subscribe requests to the list. Use the
> > >www interface or send it to gmx-users-request at gromacs.org.
> > >
> > >
> > >_______________________________________________
> > >gmx-users mailing list
> > >gmx-users at gromacs.org
> > >http://www.gromacs.org/mailman/listinfo/gmx-users
> > >Please don't post (un)subscribe requests to the list. Use the
> > >www interface or send it to gmx-users-request at gromacs.org.
> >
> >---------------------------------
> >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.)
> >
> >
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
>
> ---------------------------------
> 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.)
>
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list