[gmx-users] Some questions on itp files.

[Senthil Kandasamy]

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?


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?