[gmx-users] Water models and force fields

[Anton Feenstra]

Lieven Buts wrote:
> 
> I presume you have to run
> 
>    genbox -cp out.gro  -cs tip4p.gro   -o solv.gro   -p whatever.top
>                        =============
> 
> although this gives the following strange warning:
> 
> WARNING: masses will be determined based on residue and atom names,
>          this can deviate from the real mass of the atom type
> Opening library file
> /nurvt/programs/IRIX64_IP30/specific/gromacs-3.1.4/share/top/atommass.dat
> Mass of atom SOL MW4 set to 12.011
> ==================================

It look strange, but is not really a problem. Genbox calculates total
system mass en density as an additional service to the user, so you
can see whether the generated system is more or less acceptable. In
this case, the mass per Tip4p water will be wrongly calculated (the MW 
probably should not be counted in the mass), but this is no problem 
since it is only used to print out the system density, and not in
any part of the topology file or whatever. You could correct this by
adding a mass of 0 for MW4 to the $GMXLIB/atommass.dat

> Then the section
> 
> ; Include water topology
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> 
> would have to be changed, but I do not know exactly how.

There is a 'tip4pgmx.itp' file in $GMXLIB, so in stead of
the above, you would have:
> ; Include water topology
> #include "tip4pgmx.itp"

I don't think there are flex/non-flex variants of tip4p...

I also don't know how well-tested this tip4p implementation
is, and wheter it is exactly what it should be, and wheter it
will run with (any of) the current Gromacs version(s).

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
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