[gmx-users] .top file molecules directive

Aranha, Michelle maranha at vols.utk.edu
Thu Jul 10 17:03:45 CEST 2014


My system  consists of a carbon nanotube separating two reservoirs of water bounded by 2 graphene sheets at the interface between water and the CNT.
I build the topology after constructing this geometry using g_x2top . This gives me a file which includes all the interactions for the CNT, graphene and water but in the final directive  I have just 1 molecule, instead of 3 different molecules.
My question is can this result in artifacts in the system because of the way I'm building the top file? I checked for the bonded and non- bonded parameters in the top file and they seem correct.


More information about the gromacs.org_gmx-users mailing list