[gmx-users] Whereabouts of NDLP???
tsjerkw at gmail.com
Tue Feb 15 13:04:37 CET 2011
It has: http://haddock.chem.uu.nl/Squeeze/
On Tue, Feb 15, 2011 at 12:46 PM, ifat shub <shubifat at gmail.com> wrote:
> Was this server ever reestablished?
> Is there a link which I can use to calculate the optimal box?
> Hi Alan,
> Unfortunately there have been server problems (severe hacking) in
> Groningen some while ago, and the NDLP server was terminated. But,
> we're right about to reestablish an improved server here in Utrecht.
> This server will be much faster, seconds rather than hours - the
> optimal packing for the GroEL/GroES complex (60k atoms) took somewhere
> around a minute maybe, and will also provide an optimal simulation
> cell for a given ensemble (NMR, ENM, MD). In addition, the principal
> author at the time was not in favour of adding the program to the
> Gromacs suite, and there were some depency issues as well. I don't see
> why the new program should not also become incorporated in Gromacs.
> That being said, we still need a bit of time here to wrap things up.
> In the mean time, as long as I'm not run over by requests, you can
> send me a (few) structure(s) off the list, and I'll be happy to
> calculate the packing.
> On Sat, Mar 15, 2008 at 5:15 AM, Alan Chen <achen at artsci.wustl.edu>
>> Hi All:
>> I recently came across Tsjerk Wassenaar's JCC papers about a
>> Near-Densest Lattice Packing
>> algorithm for choosing the optimal triclinic box for a non-spherical
>> I have a rather cylindrical RNA I am studying right now, and I wanted
>> to try out NDLP only the website referred to by the paper
>> no longer exists, and I can't find any reference to NDLP on the new
>> rug.nl homepage nor does google give me any clues. Does
>> anyone know as to this package's current whereabouts?
>> Alan Chen
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> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
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Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
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