[gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics

[Joe Jordan]

Without knowing anything about your system this question is difficult to
answer. Yo should start by reading the literature on your system or related
systems and see what they do.

On Tue, Mar 20, 2018 at 8:41 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> 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,
>
> DILIP.H.N
> PhD Student
>
>
>
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-- 
Joe Jordan