[gmx-users] Implicit solvent simulation
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 18 17:08:46 CEST 2007
Stéphane Téletchéa wrote:
> Moore, Jonathan (J) a écrit :
>> I asked for and received the code a couple of years ago.
>> As the paper indicates, it's in an ancient version of GROMACS...which
>> creates challenges. Also, the different models (Still, etc.) are
>> implemented in independent versions of the code. Also, the GB part is
>> actually implemented in FORTRAN.
> You are lucky, i did so and never got the code.
> This raises the question about GPL violations and publication
> trustworthy, since it is published, can we consider the code has been
> made publicly available since provided once a paper has been published,
> we are supposed to be able to reproduce the published work.
> I had not pushed a lot for getting the code but since traces are 'still'
> in gromacs code (in every mdp-generated file at least, there is a
> mention about GB parameters), it would be nice to have an official
> statement on this from the core developpers of GROMACS.
> I'm not trying to get any grief here, if you consider this a non-issue,
> please ignore the message, that'll be enough to me.
The version used by Alan Mark has never made it into gromacs. Rather,
Erik Lindahl started the implementation of this stuff but did never
finish it completely, due to other priorities I presume. We should
however take out the variables to avoid confusion (unless someone
provides a full implementation).
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://folding.bmc.uu.se
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