[gmx-developers] adding input records
schraven at mpip-mainz.mpg.de
Sat Aug 6 20:36:45 CEST 2005
Sorry for the late reaction, but I had a similar question w. answer some
For me it worked this way, I hope it's helpful to you as well!
Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research
On Wed, 3 Aug 2005, Jason de Joannis wrote:
> Sorry about that previous post.
> > Date: Sun, 31 Jul 2005 12:13:13 +0200
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-developers] adding input records
> > To: Discussion list for GROMACS development
> > <gmx-developers at gromacs.org>
> > Message-ID: <1122804793.4466.5.camel at localhost.localdomain>
> > Content-Type: text/plain
> > On Fri, 2005-07-29 at 16:58 -0400, Jason de Joannis wrote:
> >> Dear Developers,
> >> How can I expand the parm->ir structure?
> >> I have a lot of new parameters that I want to introduce into
> >> my mdp-file, so parm->ir.userint1... are not enough.
> > How many did you think of?
> Seven integers and two reals right now.
> >> When I modify inputrec.h, tpxio.c and txtdump.c in a straightforward
> >> way (e.g. adding userint5), I get a lot of warnings during compile.
> >> "comparison between signed and unsigned". When I try to run the new
> >> program I get
> > You will also have to add kernel/readir.c, and there may be more
> Aha. I missed that one!
> > Then you'll have to make stuff conditional in tpxio.c, and increase the
> > tpx version
> There are no conditionals for e.g. userint1 so I should be fine.
> Thanks for the tpx_version tip -- I have done that.
> >> Fatal error: calloc for ir->opts.eg_excl (nelem=-1986540631, elsize=4, file
> >> tpxio.c, line 457): Cannot allocate memory
> >> How can I fix this without getting my hands dirty?
> > Now you're asking too much, but it seems your hands are slightly greasy
> > already...
> Slightly greasy is acceptable ;) I have managed to get it working.
> Incidently this requires a new grompp as well as mdrun - something that
> escaped my first notice.
> > If you are implementing something that you think would be useful for
> > others as well, then please do it in the CVS version, that will make it
> > easier to add your stuff to a future version of gmx.
> This code mutates lipid species in a semigrand-CBMC fashion. Right now
> it is capable of chopping one or both tails. We will add it to the cvs
> maybe in a little while, if anyone is interested?
> >> /Jason
> > --
> > David.
> > ________________________________________________________________________
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Jason de Joannis, Ph.D.
> Emory University
> 1515 Pierce Dr, Atlanta, GA 30329
> Phone: (404) 712-2983
> Email: jdejoan at emory.edu
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