[gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics
Dilip H N
cy16f01.dilip at nitk.edu.in
Tue Mar 20 20:41:21 CET 2018
I have run a simulation for 10 ns (0.001 * 10000000 = 10000 ps) and have
saved the data for every 0.5 ps (nstxout= 500....etc.,...) (which comes to
Since if i extract the trajectory in .gro format for the full simulation,it
will be such a huge file, so i intended to extract the trajectories having
500 frames since it will be relatively less file size. The command is:
gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrj500.gro -dt 20
which gives the full trajectory, but has 500 frames in total (ie., from
t=0ns to t=10ns, the frames are 500 with an interval of 20 ns).
So, my question is that, is this trajectory sufficient/good to analyze the
hydrogen bond dynamics (intermittent and continuous)...??
I have the trajectories extracted in .gro file for time t=0, t=20, t=40 and
so on... So the interactions/bonding is taken for t=20 ns... Is this affect
the dynamics study..??
Can anybody suggest the best possible way of trajectories (like how many
time frames/intervals etc.,) to be taken for HB Dynamics..??
Any suggestions are highly appreciated.
With Best Regards,
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