[gmx-users] Intel Compiler Options on Itanium2

Mon Jan 26 20:55:01 CET 2004

Hi,
Does any one have suggestions for compiler options (CFLAGS) to compile
gromacs on a itanium2 with intel compiler ifort and icc (version 8.0)?
Thanks

> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of Ilya Chorny
> Sent: Sunday, January 25, 2004 1:01 AM
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] cutt offs
>
>
> 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.)
> >
> >
> >
> >_______________________________________________
> >gmx-users mailing list
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> >
> >
> >_______________________________________________
> >gmx-users mailing list
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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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