[gmx-users] Binding free energy of an ion from alchemical transformation

Dear Gromacs users, I'm thinking about performing free energy calculations for a protein that binds cations, using alchemical transformation method. In the simplest case I'd transform an ion (one atom) into a naked particle; however in this case I'd get a non-zero overall charge of the system

[gmx-users] trajectory tools don't work with large .xtc / .trr files

Dear all, I've been using GROMACS successfully for quite some time on several platforms, although after a recent upgrade my main linux workstation to Ubuntu 14.04 and new installation of latest GROMACS (5.0.4) I noticed very strange behaviour of several tools (mainly trjconv and gmxcheck).

Re: [gmx-users] -vsite hydrogen

We have tested virtual sites with CHARMM36 lipids; straightforward usage gives too ordered membranes. We have created custom virtual sites construction for lipid hydrogens and used them for pure membranes as well as for membrane proteins, and the differences between membrane properties with