Are you interested in diffusive motion of your molecules or in internal
coordinate changes? For the later you need to align the trajectory to
remove translational and rotational motion, for the former you should not
align it.
For wrapping, based on the manual, the diffusion command in cpptraj does
handle imaging automatically (see the noimage keyword of that command as
well), so it can process both wrapped and unwrapped trajectories. The only
thing that seems to not work is wrapped trajectories plus the noimage
keyword.
In any case, why not try both options and see if the results make sense?
Kind Regards,
Thomas
On Wed, Dec 20, 2023 at 11:30 AM Dulal Mondal via AMBER <amber.ambermd.org>
wrote:
> **Warning** The sender address (Dulal Mondal via AMBER ) can not be
> verified, sender email address could be spoofed. Please take care to
> proceed.
> Dear Experts,
> I am trying to calculate mean square displacement using cpptraj. In the
> input file ("mdin"), I set the iwrap=1 command. Is it mandatory to unwrap
> the trajectory before analysis?
> Again, is it mandatory to align the trajectory?
>
> Thanking You
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
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--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Wed Dec 20 2023 - 05:00:03 PST
