## VMD-L Mailing List

**From:** RonitS Chem (*ronits.chem95_at_gmail.com*)

**Date:** Thu Oct 22 2020 - 14:33:57 CDT

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

Thank you for the clarification. I am using the expression I wrote in my

code for MSD, and I used the pbctools to unwrap my trajectory. Everything

looks fine for a while before I see stretched bonds, I guess it is

expected. I will play around with it till I get an acceptable set of

snapshots. Thank you again.

On Thu, Oct 22, 2020 at 12:28 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

*> you have "root mean squared deviation" versus "mean squared displacement".
*

*> it seems similar, but is not the same.
*

*> the first is a measure for how much a structure is changing, while the
*

*> other is a measure for mobility from which you can compute self-diffusion.
*

*>
*

*> On Thu, Oct 22, 2020 at 3:16 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.
*

*>
*

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