Re: [gmx-users] Topology Manipulation question

Hi! you usually get that type of output when the order in which the molecule atoms are written in the topology file (in the itp in your case) does not correspond to the order in the gro file; it might just be that you call the itp corresponding to the second molecule written in the gro file before

[gmx-users] Topology Manipulation question

Hello, I'm running grompp on two small molecules in a single .gro file using the following topology file: #include "ffgmx.itp" #include "BDEX.ITP" #include "AHL.ITP" #include "spc.itp" [ system ] BDEX AHL [ molecules ] BDEX 1 AHL 1 Part of my output looks like the following: Back O