VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Thu Oct 22 2020 - 14:50:49 CDT

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.
>>
>