## VMD-L Mailing List

**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Thu Oct 22 2020 - 15:03:21 CDT

**Next message:**McGuire, Kelly: "PBC Wrapping"**Previous message:**Josh Vermaas: "Re: Calculating mean square displacement and removing PBC"**In reply to:**Josh Vermaas: "Re: Calculating mean square displacement and removing PBC"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

that would only work, if you choose the first frame as reference. the more

typical case of using the average positions or the most likely

configuration (from cluster analysis) as reference will give you something

else.

On Thu, Oct 22, 2020 at 3:51 PM Josh Vermaas <joshua.vermaas_at_gmail.com>

wrote:

*> Yeah, point #1 confused me too. For unaligned trajectories without PBC
*

*> wrapping, computing the rmsd of your waters (for example) and squaring it
*

*> gives you a line like it should. In my experience, abusing the RMSD
*

*> calculation will give equivalent results to calculating the MSD directly.
*

*>
*

*> Josh
*

*>
*

*> On Thu, Oct 22, 2020, 1:40 PM RonitS Chem <ronits.chem95_at_gmail.com> wrote:
*

*>
*

*>> Hello Axel,
*

*>>
*

*>> Thanks for your reply. Can I get a bit more explanation about the first
*

*>> comment, from what I read MSD(t) = Sum over all i atoms (|ri(t) -
*

*>> ri(0)|**2)/N, where N is the number of atoms. And from the RMSD is just the
*

*>> square root of that expression which I read about in one of the NAMD
*

*>> ubiquitin tutorials.
*

*>>
*

*>> I will look into the pbctools plugin. Thank you again.
*

*>>
*

*>> Best,
*

*>> Ronit
*

*>>
*

*>> On Thu, Oct 22, 2020 at 11:47 AM Axel Kohlmeyer <akohlmey_at_gmail.com>
*

*>> wrote:
*

*>>
*

*>>>
*

*>>> two comments:
*

*>>>
*

*>>> 1) RMSD != sqrt(MSD) those are completely different entities.
*

*>>>
*

*>>> 2) you can use the pbctools plugin to unwrap a wrapped trajectory.
*

*>>>
*

*>>> Axel.
*

*>>>
*

*>>> On Thu, Oct 22, 2020 at 2:33 PM RonitS Chem <ronits.chem95_at_gmail.com>
*

*>>> wrote:
*

*>>>
*

*>>>> Hello all,
*

*>>>>
*

*>>>> I want to calculate the diffusion constant for a number of water models
*

*>>>> and so need to calculate the MSD from the 2ns trajectories I have. I am
*

*>>>> using my own python code, but I realize that since the periodic boundary
*

*>>>> condition is under effect I cannot calculate the distances properly.
*

*>>>>
*

*>>>> Since I use VMD to print out the snapshots for MSD calculations, is
*

*>>>> there any way to account for PBC? I would like to get rid of it, in other
*

*>>>> words get the unfolded coordinates for the atoms but I do not know how to
*

*>>>> do it. Any help or insight would be much appreciated.
*

*>>>>
*

*>>>> I have seen the RMSD tool in VMD but when I calculate the RMSD and
*

*>>>> square it to get the MSD, it is not a straight line as expected. I assume
*

*>>>> this is because of the PBC as well. I am fairly new to all this, so please
*

*>>>> forgive me if I am missing something simple.
*

*>>>>
*

*>>>> Sincerely,
*

*>>>> Ronit
*

*>>>>
*

*>>>
*

*>>>
*

*>>> --
*

*>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
*

*>>> College of Science & Technology, Temple University, Philadelphia PA, USA
*

*>>> International Centre for Theoretical Physics, Trieste. Italy.
*

*>>>
*

*>>
*

*>> On Thu, Oct 22, 2020 at 11:47 AM Axel Kohlmeyer <akohlmey_at_gmail.com>
*

*>> wrote:
*

*>>
*

*>>>
*

*>>> two comments:
*

*>>>
*

*>>> 1) RMSD != sqrt(MSD) those are completely different entities.
*

*>>>
*

*>>> 2) you can use the pbctools plugin to unwrap a wrapped trajectory.
*

*>>>
*

*>>> Axel.
*

*>>>
*

*>>> On Thu, Oct 22, 2020 at 2:33 PM RonitS Chem <ronits.chem95_at_gmail.com>
*

*>>> wrote:
*

*>>>
*

*>>>> Hello all,
*

*>>>>
*

*>>>> I want to calculate the diffusion constant for a number of water models
*

*>>>> and so need to calculate the MSD from the 2ns trajectories I have. I am
*

*>>>> using my own python code, but I realize that since the periodic boundary
*

*>>>> condition is under effect I cannot calculate the distances properly.
*

*>>>>
*

*>>>> Since I use VMD to print out the snapshots for MSD calculations, is
*

*>>>> there any way to account for PBC? I would like to get rid of it, in other
*

*>>>> words get the unfolded coordinates for the atoms but I do not know how to
*

*>>>> do it. Any help or insight would be much appreciated.
*

*>>>>
*

*>>>> I have seen the RMSD tool in VMD but when I calculate the RMSD and
*

*>>>> square it to get the MSD, it is not a straight line as expected. I assume
*

*>>>> this is because of the PBC as well. I am fairly new to all this, so please
*

*>>>> forgive me if I am missing something simple.
*

*>>>>
*

*>>>> Sincerely,
*

*>>>> Ronit
*

*>>>>
*

*>>>
*

*>>>
*

*>>> --
*

*>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
*

*>>> College of Science & Technology, Temple University, Philadelphia PA, USA
*

*>>> International Centre for Theoretical Physics, Trieste. Italy.
*

*>>>
*

*>>
*

-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.

**Next message:**McGuire, Kelly: "PBC Wrapping"**Previous message:**Josh Vermaas: "Re: Calculating mean square displacement and removing PBC"**In reply to:**Josh Vermaas: "Re: Calculating mean square displacement and removing PBC"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]