[gmx-users] gromos function type assigned by grompp

Romelia Salomon romelia at caltech.edu
Thu Aug 7 01:22:03 CEST 2008


I am trying to set a calculation based on the GROMOS force field in a
program I have and I am using GROMACS to generate the (starting) input
files for me. From reading the manual I know that GROMOS uses a fourth
power potential (type 2) for bonds and a cosine based angle potential
(type 2), but I noticed that when using grompp to include the values for
the parameters explicitly it changes the type from 2 to 1, for example:

topology file before grompp
[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     2    gb_2
    1     3     2    gb_2
    1     4     2    gb_2
    1     5     2    gb_20
    5     6     2    gb_26
    5    10     2    gb_26
after using grompp
[ bonds ]
;  ai    aj  tp parameters
    N    H1   1       0.1 1.87e+07
    N    H2   1       0.1 1.87e+07
    N    H3   1       0.1 1.87e+07
    N    CA   1     0.147 8.71e+06
   CA    CB   1     0.153 7.15e+06
   CA     C   1     0.153 7.15e+06

Is this right? Also, for clarification, I know Gromacs uses kj/mol and nm
as units, so does that mean that the values included in the ff*.itp files
under the share/top/ directory are in those units?

Also I noticed that the .itp files for bonding interactions in gmxbon.itp
have declared a type 1 function which would be the regular harmonic one.

Sorry for the very basic questions, but I wanted to be certain about this
things, thanks!!



Romelia Salomon
Miller Group
316 Noyes
Chemistry Department

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