From: Krishna Vkm (
Date: Mon Sep 07 2020 - 04:56:11 CDT

Hi John
Thank you for your suggestions.
Actually I am calculating some distance (I just briefly mentioned to peter
in this mail), and the distance itself is very random. Repeating the
simulations results in different values of distance. So if I compare the
distance from simulations using both versions of namd, it will be difficult
for me to say whether they are different or similar.

On Mon, Sep 7, 2020 at 3:31 AM Josh Vermaas <>

> 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 <> 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*