[gmx-users] regarding MSD

[Nidhi Katyal]

Please reply.

Reposting the same query again:

I have read few papers that determine transition temperature from the plot
of average MSD of hydrogen atoms of protein versus temperature. My question
is:
At a particular temperature, we get a linear curve for MSD versus time, is
it reasonable to calculate average MSD over all such time points? Is this
the average that is plotted in papers (or something is missing) ? My doubt
is won't this average depend on the number of time points (due to its
linear nature)?

Actually I am trying to reproduce the results of some published data.
Although I am getting the same transition temperature but the MSD values
are coming different (eg at a particular temperature if I average all the
MSD values, I am getting value of 15000 while reported value is 1.5 - both
values in same unit angstrom square)




On Fri, Aug 22, 2014 at 7:15 PM, Nidhi Katyal <nidhikatyal1989 at gmail.com>
wrote:

>
>
> ---------- Forwarded message ----------
> From: Nidhi Katyal <nidhikatyal1989 at gmail.com>
> Date: Fri, Aug 22, 2014 at 11:41 AM
> Subject: Re: regarding MSD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>
> Hello
>
> I have posted the query earlier but havent got any reply and so reposting
> it again.
>
> I have read few papers that determine transition temperature from the plot
> of average MSD of hydrogen atoms of protein versus temperature. My question
> is:
> At a particular temperature, we get a linear curve for MSD versus time, is
> it reasonable to calculate average MSD over all such time points? Is this
> the average that is plotted in papers (or something is missing) ? My doubt
> is won't this average depend on the number of time points (due to its
> linear nature)?
>
> Actually I am trying to reproduce the results of some published data.
> Although I am getting the same transition temperature but the MSD values
> are coming different (eg at a particular temperature if I average all the
> MSD values, I am getting value of 15000 while reported value is 1.5 - both
> values in same unit angstrom square)
>
> Any help is highly appreciated.
>
>
>
> On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal <nidhikatyal1989 at gmail.com>
> wrote:
>
>> Hello all
>>
>> I have read few papers that determine transition temperature from the
>> plot of average MSD versus temperature. My question is:
>> At a particular temperature, we get a linear curve for MSD versus time,
>> is it reasonable to calculate average MSD over all such time points? Is
>> this the average that is plotted in papers (or something is missing) ? My
>> doubt is won't this average depend on the number of time points (due to its
>> linear nature)?
>> Any help is highly appreciated.
>>
>> Thanks
>> Nidhi
>>
>
>
>