## VMD-L Mailing List

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

**Date:** Thu Oct 22 2020 - 14:16:06 CDT

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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.
*

*>
*

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