[gmx-users] Need guidance

Lovika Moudgil lovikamoudgil at gmail.com
Wed May 21 06:45:24 CEST 2014

Hi Everyone,
Need guidance and help.....
As I am doing md simulation for Lysozyme in presence of gold i.e Au(111)
with force field oplsaa and Golp parameters . What I am doing is first
generating .top file for protein with oplsaa force field  and then using
Golp gold .itp and .gro file parameters adding them to protein generated
.top file. The .itp files for gold , I am adding are of surface ,bulk
,virtual . Coordinates that I am using are all taken from Golp force field
.gro file . Mdp file that I am using is also from Golp in which Au and AUI
Group is freezed. Changes that I am making are in .top file generated by
pdb2gmx and adding gold coordinates to the protein.pdb file .But my system
is giving error in  grompp ....  The sum of the two largest charge group
radii is larger than rlist .... or DD cell error .. Please guide me where I
am wrong ..Is there any thing serious that I am missing in my system .

Please guide...

Thanks and Regards

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