[gmx-users] g_hbond

2010-09-17 Thread Fahimeh Baftizadeh Baghal
hello, I have a trajectory generated by gromacs in which I excluded water and there is only protein, now I like to see how does the number of h_bond between water and protein change during the trajectory. In fact when I use g_hbond I can choose the water and protein but I was wondering where

[gmx-users] strange jumping in the frames

2010-09-10 Thread Fahimeh Baftizadeh Baghal
I am running Metadynamics with gromacs, I saw a jump in the frame after the simulation was running for a while, I copy here part of the log file: Step Time Lambda 2055750041115.00.0 Energies (kJ/mol) AngleProper Dih.