On Wed, May 22, 2013 at 8:05 PM, rajat desikan wrote:
> Thanks for the reply,
> trjconv does not have any bugs in removing pbc, right? We can just feed the
> -nojump output to g_msd.
>
Maybe. There are not (yet) any automated tests for the code in these tools.
But probably trjconv -nojump works c
Thanks for the reply,
trjconv does not have any bugs in removing pbc, right? We can just feed the
-nojump output to g_msd.
I am going to output the coordinates and velocities with g_traj and run it
through my own code :)
On Wed, May 22, 2013 at 11:19 PM, Mark Abraham wrote:
> Along the lines of
Along the lines of take a trajectory, and look through it for a frame where
it crosses the periodic boundary of the original cell. Look for artefacts
in the analysis at that time. Or take that frame and use it as a reference
state for whatever trjconv-based PBC-massaging workflow you previously use
Hi Mark,
Regarding your statement, how does one check whether g_msd has removed pbc
correctly or not?
Thanks
On Wed, May 22, 2013 at 10:56 PM, Mark Abraham wrote:
> On Wed, May 22, 2013 at 4:49 PM, Yutian Yang wrote:
>
> > Erik,
> >
> > Do you mean that if the particle diffuses too fast, it wil
On Wed, May 22, 2013 at 4:49 PM, Yutian Yang wrote:
> Erik,
>
> Do you mean that if the particle diffuses too fast, it will appear like it
> doesn't move because of the PBC?
>
Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect
I have another issue. If I have a polymer chain with the length
Erik,
Do you mean that if the particle diffuses too fast, it will appear like it
doesn't move because of the PBC?
I have another issue. If I have a polymer chain with the length almost the same
as the box length. It is possible that the COM diffusion of the chain may
appear it does not move
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