[gmx-developers] adding input records
Jason de Joannis
jdejoan at emory.edu
Wed Aug 3 22:27:10 CEST 2005
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
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?
> 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.
1515 Pierce Dr, Atlanta, GA 30329
Phone: (404) 712-2983
Email: jdejoan at emory.edu
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