[gmx-users] Some questions on itp files.

[Anton Feenstra]

Senthil Kandasamy wrote:
> I have a few nagging doubts that need to be clarified.
> 
> 1. The parameters specified in the molecule.itp file override those in
> the ffgmx*.itp. Is that correct? e.g. in urea.itp
> 
> [bonds]
> 3   4 	1	1.000e-01	3.744e+05
> ...
> 
> Here b0 and kb from this file are used rather than the values in
> ffgmxbon.itp.  If I do not specify these values, then the values from
> ffgmxbon.itp will be used. correct?

Absolutely.

> 2. [pairs]:
> 
> If I specify a pair of atoms under the pairs directive, then the 1-4 non
> bonded interactions "ARE" calculated. If C6 and C12 are zeros, then this
> effectively means that the LJ interaction is zero, but coulombic forces
> will be calculated. Am I correct?

Close, actually the 1-4 LJ is a bonded interaction in Gromacs, and it
has it's own directive in the ff*bon.itp under [ pairtypes ]. Check
the manual, this is actually rather well and thoroughly described!


-- 
Groetjes,

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