[gmx-users] MD - analysis
Kavyashree M
hmkvsri at gmail.com
Mon Jun 13 13:44:42 CEST 2011
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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