Hi all
Can someone please help?
For a complex with 2 chains (protein-protein), 2 itp files (posre_Protein_chain_A.itp and posre_Protein_chain_B.itp) are generated using pdb2gmx. So during equilibration, are both itp files considered by default?
If you look at the topology entries, they are conditional, i.e. embedded in an #ifdef/endif pair. So if they are locally available, they will be included/turned on during gmx grompp processing if your .mdp file has the define = -DPOSRES entry (assuming POSRES this is the condition), and ignored/turned off otherwise.
Thank you, I understand it now.