[gmx-users] (no subject)

[shakuntala dhurua]

Thank you sir for your suggestions

On Fri, 8 Nov 2019, 7:31 pm Christian Blau, <blau at kth.se> wrote:

> Hello Shakuntala,
>
>
> If you already have the trajectories, you have to post-process at least
> once to filter the data down to a manageable
> size, and once to do the periodic boundary condition fix precisely as you
> described.
>
> If you set up a new simulation you may use "nstxout-compressed" to control
> the output frequency for your xtc file. It is
> very unlikely that you will need a .trr file, so you can even set nstxout,
> nstvout and nstfout to zero. Starting your
> post-processing from a xtc should speed up your analysis process.
>
>
> On another note: Please fill in a subject line in your emails, it makes it
> easier to search and keep track of the
> ongoing discussions.
>
>
> Best,
>
> Christian
>
>
> On 11/7/19 3:12 PM, shakuntala dhurua wrote:
> > I would like to calculate rmsd of protein system, but there is much time
> > taking for trjcat of all simulated trajectories (.trr file) then
> generated
> > .xtc file by using -center -pbc mol flag. from this .xtc file i use to
> > calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I
> > want to ask here is any other way is available to directly calculate rmsd
> > without using trjcat or less time taking method.
> --
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