[gmx-users] mdrun

Dear all, I am trying to run dynamics (mdrun) on GROMACS 4.5.3 in parallel on 8 processors, but it crashes after a while and refuses to reach to the end. The error note that pops out is: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off >> out of the domain decomposition

[gmx-users] Questions regarding REMD simulation

Hi All, I have few questions regarding REMD simulation. I assume REMD works in the following way: Each replica starts with a given temperature and the temperature of each replica changes along the simulation (as described in Sugita and Okamoto publication, 1999). Then demux.pl and trjcat collect

[gmx-users] shell molecular dynamics

Hello, I would like to run a simulation using the shell option. I tried to restraint solvent molecules which were found within the range of 5-10 angstroms from the box center. I couldn't find any way to do so. I didn't find any information about this topic anywhere else i.e. GROMACS manual, onlin