[gmx-users] itp atomtypes section

James Cannon jamesresearching at gmail.com
Tue Nov 27 03:45:07 CET 2012

Dear users,

I apologise if this is a stupid question, however after a morning of
searching I have not been able to find the answer.

1. I have a sample itp file and it contains a section like this:
[ atomtypes ]
    CF      CF  6  12.01100    0.2588       A    3.50000e-01  2.56134e-01
    HF      HF  1   1.00800    0.1000       A    3.50000e-01  4.28529e-01

I can't work out what the column containing the "6" and "1" is for. Can
anyone help? It's not documented anywhere that I can find.

2. I notice that there are many types of "atomtypes" fields. From the
[ atomtypes ]
;name mass charge ptype c6 c12
O 15.99940 0.000 A 0.22617E-02 0.74158E-06
OM 15.99940 0.000 A 0.22617E-02 0.74158E-06

This is clearly a different format to my sample above. Why does the format
vary? I know the above format is not wrong because it runs succcessfully in
a test-run. How does gromacs know which format to use correctly?

I appreciate any help.
Thank you.
Best regards,


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