[gmx-users] cutt offs
ichorny at maxwell.compbio.ucsf.edu
Wed Jan 7 22:20:01 CET 2004
I currently have both cutoffs LJ and Couloumb cutoffs set 1.5 nm. The
energy of the water in 10% more stable and more dense with a 1.5 nm LJ
cutoff then a .8 nm LJ cutoff. This causes the solvation free energies
to increase dramatically about 50 % in some cases. Any advice on how to
So that I can have a different cuttoffs for the solute-h2o than h20-h20.
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
On Behalf Of David
Sent: Wednesday, January 07, 2004 12:11 PM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] cutt offs
On Wed, 2004-01-07 at 21:58, Ilya Chorny wrote:
> So what do I do when I have a solute that has a 1nm radius?
Is this still your single particle? In that case there is a problem,
otherwise each charge group in your molecule sees every water within the
cut-off... The twin range takes care of the long range forces. Don't
know about long range free energy contribution...
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
> On Behalf Of David
> Sent: Wednesday, January 07, 2004 12:01 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] cutt offs
> On Wed, 2004-01-07 at 21:45, Ilya Chorny wrote:
> > I ran a whole new set of calculations calculating the solvation of
> > molecules in SPC. I get significantly different results if I use a
> > cutoff distance of 1.4 for the LJ vs .8. I always assumed that the
> > interaction falls off much faster than that but I guess I was
> > the Jacobian. Do other people see this kind of effect? The SPC water
> > becomes significantly more stable with the larger cutoff distances I
> > think this is where it would be useful to have a cutoff distance
> > different for the solute then the solvent. What cutt off distances
> > SPC parameterized for?
> 0.9 nm.
> However, the latest GROMOS proten force field is parameterized for
> twin/range 0.8/1.4 although most people probably run it with 0.9/1.4.
> (Oh, and nstlist should be 5 steps of 2 fs with shake).
> > Thanks
> > Ilya
> > _______________________________________________
> > 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 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
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users