[gmx-users] Handling a very large system
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jul 22 09:00:01 CEST 2005
On Thu, 2005-07-21 at 16:23 -0400, Ken Rotondi wrote:
> Thanks David,
> Excuse me, I did mean...
> constraints = all-angles
> I had read about the issues with LINCS. Is it possible to apply the
> constraints to a sub-set of the system?
not automatically, you have to supply a list of constraints then
> On Jul 21, 2005, at 4:06 PM, David wrote:
> > On Thu, 2005-07-21 at 15:55 -0400, Ken Rotondi wrote:
> >> 2) I can constrain all angles in the system using:
> >> constraints = all bonds
> > this would constrain bonds only, which is fine. constraining angles
> > gives problems with the LINCS algorithm although it may work with
> > SHAKE.
> >> in my .mdp file. Is it possible to apply these restraints to a sub-set
> >> of all residues in the system?
> K.S. Rotondi Ph.D.
> Research Fellow
> The Gierasch Laboratory
> Department of Biochemistry and Molecular Biology
> University of Massachusetts-Amherst
> Phone: 413-545-1250
> Fax; 413-545-3291
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David van der Spoel, PhD, Assoc. 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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