[gmx-users] charmm36M generated topology conversion to GROMOS54A7 ff

hi users, I generated ligand topology containing complex metals using ATB server, developed using GROMOS54A7 modified forcefield. Then i used Charmm gui for protein embedding in lipid bilayer followed by catenation of both .gro files. System was solvated but during ion addition it couldnot

[gmx-users] Simulation of membrane associated protein

Dear all, I am working on DOPC-associated protein and try to orient the protein on the DOPC surface by using the gmx_solvate as previously suggested by Prof. Justin Lemkul at the following like http://www.mdtutorials.com/gmx/biphasic/03_tricks.html

[gmx-users] Extracting trajectory

Dear users, I want to extract the trajectory of water molecules near the protein surface within 5 angstorm region. I was able to do that in using gmx select and gmx trjcat, but it is for only one time frame and than the water molecules diffuses away for the next time frame. I want to extract the

[gmx-users] how to calculate average structure

Dear all; I performed a molecular dynamic simulation(50ns) for a complex aptamer-ligand and I am going to analysis the interaction between aptamer and ligand during the simulation,then I will need the average structure. How can I calculate the average structure, is it correct to use the

[gmx-users] GROMACS 2019.4 patch release available

Hi GROMACS users, The official release of GROMACS 2019.4 is available! The fourth patch release fixes several issues found since the previous patch release of GROMACS 2019. We encourage all users of the 2019 series to update to 2019.4. Please see the link to the release notes below for more