[gmx-users] MD - analysis

[Kavyashree M]

Dear Sir,

  Thanks for your reply.

It means "not a number."  I've never seen that before from g_energy, but
> based on the extremely small error estimates, especially for the
> temperature, I'd suspect you're using extremely tight coupling which may be
> causing some error.


I was thinking such errors come when there are some infinite values.  This
same
mdp file parameters I have used to run 3 more simulations in different
systems.
But that was all fine, such "nan" error was not present.


> The RMSD presented by g_energy is the standard deviation of the data
> analyzed. It is unrelated to the RMSD of the protein.


Yes that is true. I just checked it to make sure that there is no horrible
errors in
the trajectory.

In a periodic system, there is no such thing as "inside" and "outside" since
> the system is infinite.
>

Than is true. but why  mentioned is that when we are analyzing we take into
account only one of the unit cell not infinite. By outside I meant out of
the unit
cell in consideration into a periodic image.

 trjconv -pbc mol -ur compact (and -center if you like).


Thank you I will try it out.

 Never used ngmx, but with the trjconv command I've stated everything should
> show up quite nicely in VMD :)
>

Ok thanks. I am new to VMD need to explore it more.

Thanking you
With Regards
M. Kavyashree
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