VMD-L Mailing List

From: RonitS Chem (ronits.chem95_at_gmail.com)
Date: Thu Oct 22 2020 - 14:16:06 CDT

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.
>