VMD-L Mailing List

From: RonitS Chem (ronits.chem95_at_gmail.com)
Date: Thu Oct 22 2020 - 14:33:57 CDT

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.
>