## VMD-L Mailing List

**From:** Josh Vermaas (*joshua.vermaas_at_gmail.com*)

**Date:** Thu Oct 22 2020 - 14:50:49 CDT

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

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.
*

*>>
*

*>
*

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