[gmx-users] conversion to tip5p

Manik Mayur manik.mayur at gmail.com
Fri Jun 5 15:46:37 CEST 2009

2009/6/5 Dmitri Dubov <ddubov at ngs.ru>

>  Hi, all
> Using gromacs 3.3 I try to work with tip5 water, but I fail to convert
> water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is
> easy with pdb2gmx
> pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top
Does it really converts like that? I mean will it adjust the bonds and add a
dummy atom just like that?

>  , but when I apply similar command for tip5p, the output gro-file
> contains only four-point water molecules.
> Could anyone help me?
> --
> Regards,
>  Dmitri                          mailto:ddubov at ngs.ru <ddubov at ngs.ru>
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Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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