[gmx-users] lipid bilayer and umbrella sampling

Dear Gromacs Users,     I am trying to extract the potential of mean force of a small molecule in a DPPC bilayer. To this end, I applied the methodology described in an online manual written by Justin Lemkul. My problem is when I run biasing simulations of the molecule near the interface (DPPC

[gmx-users] CHARMM 36 force field

Dear Tom,     Thank you very much for your answer. I am aware of the paper you suggested but it is not clear for all mdp parameters. My intent is the simulation of a small organic molecule into the DPPC membrane making use of the CHARMM36 force field. There are significant differences when I c

[gmx-users] CHARMM36 force field

Dear GROMACS users,     I am interested in simulating a DPPC membrane with CHARMM 36 force field in GROMACS. The charmm36.ff_4.5.4.tgz was downloaded by the following web page: http://www.gromacs.org/Downloads/User_contributions/Force_fields. When the membrane is simulated in NPz(A=0.64nm^2)