[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
> 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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