[gmx-users] (no subject)

[Christian Blau]

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.