Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

Dear Yujie Liu, Can I clarify your suggestions? copy gly.gro into protein.gro and changed the number of atoms: ) After running "gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o protein_glycine.gro", the "protein_glycine.gro" already contains both protein residues and glycine

Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

But what if the coordinates do not match? I mean Glycine may not have the same coordinates after. On Mon, Aug 7, 2017 at 2:48 PM, yujie liu wrote: > > The .top file of protein has included itself all parameters, so now you > only copy gly.gro into protein.gro and changed

[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

Dear Gromacs, I am doing a MD for a protein with glycines. For glycine, I use ) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter and got ) gly.gro ) posre_gly.itp ) topol_gly.top For protein, I use ) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh