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

[Mark Abraham]

Hi,

And doing the reading and planning for your data collection *before*
collecting data is a really great strategy.

Mark

On Wed, Mar 21, 2018 at 8:44 AM Joe Jordan <e.jjordan12 at gmail.com> wrote:

> 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
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