Re: [gmx-users] comm-grps for a membrane-protein-ligand system

Peter C. Lai wrote: Ok thanks My primary concern is to cancel membrane-protein drift - the protein getting pushed to one side of the membrane box (also it's important for me to have the protein stay centered in the box too). I have not seen There is no "center" to a periodic system. Molecu

Re: [gmx-users] comm-grps for a membrane-protein-ligand system

Ok thanks My primary concern is to cancel membrane-protein drift - the protein getting pushed to one side of the membrane box (also it's important for me to have the protein stay centered in the box too). I have not seen stability issues otherwise with COM turned on in the case of the unbound pr

Re: [gmx-users] comm-grps for a membrane-protein-ligand system

Peter C. Lai wrote: Should I couple a ligand associated with a membrane protein to the same COM group as the Protein_POPC group? It makes sense to me that would be the case since if we are investigating the interaction between protein+membrane and ligand we want to have the same COM correctio

[gmx-users] comm-grps for a membrane-protein-ligand system

Should I couple a ligand associated with a membrane protein to the same COM group as the Protein_POPC group? It makes sense to me that would be the case since if we are investigating the interaction between protein+membrane and ligand we want to have the same COM correction vector applied to both