[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

Hello all,

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
20000 frames...).
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.

Thank you.
With Best Regards,

PhD Student

<https://mailtrack.io/> Sent with Mailtrack

More information about the gromacs.org_gmx-users mailing list