[gmx-users] water shell model

[David van der Spoel]

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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-- 
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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