[gmx-users] Generation of 1-4 nonbonded parameters for CHARMM ff

Hello,I'm trying to use CGENFF to generate CHARMM topology and parameter for a small molecule, and then convert the topology with charmm2gromacs program. I have some questions on the process. 1) How is the 1-4 parameters generated from the CGENFF file? I was not able to find the parameters

[gmx-users] A question on REMD result analysis

Dear Gromacs users, I’m trying to run a REMD simulation on a protein. After a lot of reading, I am still unclear on the result analysis. Is it correct that, of many replicas, I should select the frames from only the replica with my desired temperature?(ex, room temp.) If not correct, how do I s

[gmx-users] Ligand-Protein interaction with energy groups

Greetings all, I am trying to compare the stability of two protein-ligand systems where ligands differ. I am trying to observe the difference of interaction energy between the ligands. Would it be correct to make energy groups of Protein, Solvent, Ligand, and compare the energy obtainable by g_