VMD-L Mailing List

From: Krishna Vkm (krishnatifr_at_gmail.com)
Date: Mon Sep 07 2020 - 08:04:08 CDT

Thank you for the information.

On Mon, 7 Sep 2020, 18:01 Peter Freddolino, <petefred_at_umich.edu> wrote:

> In *most* cases you should get compatible results because the physics are
> *mostly* the same, but there may be some edge cases where differences would
> arise -- for example, I'm pretty sure that a bug in long-range vdW
> corrections was fixed between 2.9 and 2.13, which would affect the physics
> for large systems if you have vdW tail corrections on (you should be able
> to see other changes by browsing the release notes). But even if you can't
> identify a particular reason why the results would be different, if it were
> me, I'd be going out of my way to use a consistent version for all
> calculations going into a single study. This might mean a conversation with
> the folks administering your cluster to see if they can make the older
> version available again as well, or setting up your own installation of 2.9.
> Best,
> Peter
>
> On Mon, Sep 7, 2020 at 5:48 AM Krishna Vkm <krishnatifr_at_gmail.com> wrote:
>
>> 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*
>>>>>
>>>>>
>>>>>