Re: [gmx-users] virtual sites for ligands?

Hi, No, you'll have to build such a topology yourself Mark On Fri., 12 Jul. 2019, 19:21 Carlos Navarro, wrote: > Dear gmx-users, > Is there a way to create a vsite-H topology of a ligand using gromacs > (pdb2gmx)? > Best regards, > Carlos > > —— > Carlos Navarro Retamal > Bioinformatic

Re: [gmx-users] convergence of bilayer simulation

Dear Justin, Thank you for your inputs. After using GridmatMD. I obtained the following results - Area per lipid is 62.696275 ± 0.545 Angstrom (square) Average thickness of the upper and lower membranes is 3.66 ± 0.28 Angstrom (square) I am also attaching the graphs for lateral displacement of

[gmx-users] virtual sites for ligands?

Dear gmx-users, Is there a way to create a vsite-H topology of a ligand using gromacs (pdb2gmx)? Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N,