[gmx-users] Intermolecular RDF in DPPC

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 4 23:41:11 CEST 2010

prithvi raj pandey wrote:
> 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 
> /export/softexport/gromacs/share/gromacs/top/ffG53a6.itp
> Opening library file 
> /export/softexport/gromacs/share/gromacs/top/ffG53a6nb.itp
> Opening library file 
> /export/softexport/gromacs/share/gromacs/top/ffG53a6bon.itp
> 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?

You're probably running out of memory.  Generating that many exclusions will 
take up a lot of resources.  Beyond that, you don't need 49 exclusions for DPPC. 
  50 atoms does not imply the longest distance between two atoms is 49 bonds.  I 
believe, for DPPC, the maximum you need should be 25.  If you only need to 
exclude interactions through the carbonyl, that number drops to 9 or so.


> -- 
> Prithvi Raj Pandey


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list