[gmx-users] how to define a pair

Hi, I am performed a all-atom simulation of a membrane-protein system (the starting structure received from CHARMM-GUI server, using charmm36 FF).  #include "toppar/charmm36.itp"   [ defaults ]; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 2 yes 1.0 1.0 I want to add a pair between list of two

[gmx-users] how to define a pair

Hi, I am performed a all-atom simulation of a membrane-protein system (the starting structure received from CHARMM-GUI server, using charmm36 FF).  #include "toppar/charmm36.itp" [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 I want to add a pair between list of two

[gmx-users] PMF ligand membrane protein

Dear Gromacs User, this is the first time I am attempting membrane protein simulation. I wish to obtain a PMF value for a ligand permeating through a membrane protein (lacY permease). In the Xray str. the ligand is almost at the center of the protein. I wish to generate enough initial

[gmx-users] apply restraints between CoM similar to distance restraints

Hi,I have  a protein which is a dimer. I would like apply a harmonic restraints such that between 0A to 10A (Angstrom) it is zero, and above 10 a harmonic potential is applied. In other words,is there a way to implement restraints between Center of Mass of two chains in a way similar to