VMD-L Mailing List

From: Krishna Vkm (krishnatifr_at_gmail.com)
Date: Mon Sep 07 2020 - 04:47:50 CDT

Hi Peter
Yes, you pointed out the main issue. I have to write that I have used
different versions of NAMD in the method section. So, I think the reviewer
can ask that there can be an issue with using different NAMD versions
regarding reproducibility.
The main thing is that I am studying a protein complex system consisting of
two proteins (let's say A and B). I am looking at the distance between the
center of mass of A and B. I ran multiple independent simulations and I
got different distances every time. Now I want to add more number
independent simulations for better statistics because the distances between
A and B are not consistent and so require good statistics. Now if different
versions of NAMD differ in some aspects ( which I am not aware of) which
can affect the distances between A and B, then I think it will be a problem
if I mix the simulations from NAMD2.9 and NAMD2.13 to know about the
distances between A and B.

Thank you

On Mon, Sep 7, 2020 at 5:30 AM Peter Freddolino <petefred_at_umich.edu> wrote:

> With that said... do you really want to write in your methods section that
> you used different versions of namd for your different simulations?
> Best,
> Peter
>
> On Sun, Sep 6, 2020 at 7:44 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
> wrote:
>
>> I would expect both versions to sample the same ensemble. Is that not
>> what you are seeing? I'd also recommend 2.14 while you are at it.
>> Josh
>>
>> On Sun, Sep 6, 2020, 4:03 PM Krishna Vkm <krishnatifr_at_gmail.com> wrote:
>>
>>> Dear NAMD User
>>> I did multiple all-atom MD simulations of my protein system two years
>>> ago with *NAMD2.9*. Now I want to do more simulations of the same
>>> system but my cluster has *NAMD2.13* instead of *NAMD2.9*. I would like
>>> to have your suggestions on whether the results from NAMD2.9 and NAMD2.13
>>> will be different or the same.
>>>
>>>
>>> *Thanks and regards*
>>> *Krishna Kant*
>>> *TIFR Mumbai*
>>>
>>>
>>>