[gmx-users] Intermolecular RDF in DPPC

prithvi raj pandey pandeyprithviraj at gmail.com
Wed Aug 4 22:04:27 CEST 2010

Dear gmx users,

I want to calculate intermolecular RDF between N and carbonyl oxygen atoms
in a DPPC bilayer. As suggested in some mails in the mailing list i wanted
to generate one tpr file for the purpose containing exclusion 49 (as united
atom model of DPPC contains 50 atoms). But while generating the tpr file
using the following command

grompp -f grompp.mdp -p topol.top -c dppc08.pdb -o rdf.tpr

the grompp program hangs saying

checking input for internal consistency...
processing topology...
Opening library file
Opening library file
Opening library file
Opening library file /export/softexport/gromacs/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations
Opening library file /export/softexport/gromacs/share/gromacs/top/spc.itp

Excluding 49 bonded neighbours molecule type 'DPPC'

and does not proceed further. What is wrong? Can anyone please help?

Prithvi Raj Pandey
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