[gmx-users] ATP parameters

[Anton Feenstra]

Paul Barrett wrote:
> Thankyou for your kind reply.
> 
> Genbox also uses these files, e.g. from the output of Genbox
> 
> Opening library file
> /lmb/flint/barrett/local/share/gromacs/top/atommass.dat 
> 
> 
> If I did not make these changes I got a lot of assignments of the form
> Mass of Atom ATP APG 12.011  i.e. the mass of all the atoms of ATP was
> apparently set to 12amu.
> 
> Was this an assignment of some other mass than the one used in the MD
> simulation?

Yes; as an extra, genbox calculates the final density in your box,
obviously it needs to know the mass of the atoms. Since it doesn't
read the topology & forcefield info, it makes a guess from the atom
names and using atommass.dat. This doesn't influence the masses used
in the simulation.

The vdwradii.dat can be important, since they determine the overlap
that genbox calculates with water.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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