[gmx-users] water shell model
David van der Spoel
spoel at xray.bmc.uu.se
Wed Aug 16 09:27:30 CEST 2006
Luciano Costa wrote:
> Hi all and Spoel
>
> Based on mailing list answer at Mar 20th 2003, which discribed the
> entire topology file for water shell model, referencing on J. Phys. Chem
> B. 105 (2618) 2001, I have tryed to run water polarization MD with this
> file.itp. However, running grompp a message "Water polarization should
> now be listed under [ water_polarization ]" appears. In my *.top file I
> wrote:
>
> #include "shell.itp"
> [ system ]
> Water
> [ molecules ]
> SW 500
>
> And shell.itp is the same as reported in the cited mailing list. An
> additional message was: "Source code file: topdirs.c, line: 145". At
> this line, in source code, I was able to see that this error probably
> comes from POSRES defintion. As can be seen below:
>
> switch (type) {
> case 1:
> return F_POSRES;
> case 2:
> gmx_fatal(FARGS,"Water polarization should now be listed under [
> water_polarization ]\n");
> default:
> gmx_fatal(FARGS,"Invalid position restraint type %d",type);
> }
>
> Can anyone help me to solve this problem?
>
see attach, the itp file is also in your share/gromacs/top directory
(i.e. $GMXLIB). Note that there are newer models from the Roux and van
Gunsteren groups that work in gromacs as well, and that you should
consider for your work.
>
> regards
>
> Luciano
> --
> ### Luciano Tavares da Costa ###
> Laboratory of Molecular Spectroscopy
> ## IQ - University of Sao Paulo - Brazil ##
> http://lem.iq.usp.br;ltcnikit@gmail.com
> <http://lem.iq.usp.br;ltcnikit@gmail.com> ##################################
>
>
>
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>
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--
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://folding.bmc.uu.se
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