[gmx-users] g_hbond seems to detect different hbonds in the same trajectory

Dear users, I computed the hydrogen bonds between solvent and protein in a 200 ps fraction of a MD trajectory with g_hbond in two different ways: in a single step with the command: g_hbond -b 400 -e 600 -hbn -hbm -g 400_600.log -num -n file.ndx -s file.tpr -f file.xtc in four steps with the comm

[gmx-users] Parrinello-Rahman coupling and constant slight evolution of box sides

Hello gmx users, I am working with gmx version 3.3.1 and i am using the ffG43A2x force field. I am currently running 4 simulations : - In 2 simulations the system is a POPE bilayer in water (454 pope with 15800 spc water molecules) - In the 2 other simulations a protein is embedded in the bilayer