Hi,
The simplest explanation for this is that one set of runs used position
restraints and one set did not.
Mark
On Mon, 29 Feb 2016 08:48 SAPNA BORAH wrote:
> hi
> Thanks for the suggestion. I will give this a shot, and remove these
> restraints.
>
> I am unclear about what should I be lookin
On 29 February 2016 at 08:48, SAPNA BORAH wrote:
> hi
> Thanks for the suggestion. I will give this a shot, and remove these
> restraints.
>
> I am unclear about what should I be looking in the log file as you
> mentioned. The conformations are not just close, they are the same as the
> initial c
hi
Thanks for the suggestion. I will give this a shot, and remove these
restraints.
I am unclear about what should I be looking in the log file as you
mentioned. The conformations are not just close, they are the same as the
initial conformation.
I have some understanding on pbc that serves a pro
Hi,
Looks like you might be applying positional restraints (define =-DPOSRES in
your mdp file). This is standard practice for equilibration, but I don't
think you want to be doing this for your production run, as this will
restrain your protein to conformations rather close to your starting
conform
Dear Mark,
I have still not been able to solve my problem. A whole new problem has now
arisen. I am listing them as follows:
1. I am running 100ns simulations for 6 protein models and I was using both
version 4.6.5 and 5.0.4 when I found that after production run, my protein
models are behaving d
Hi Sapna,
The list doesn't allow attachments. Please put them somewhere online and
provide a link.
The differences can be large. Can't tell if you don't know the possible
range of conformations/trajectories for one Gromacs version.
Did you ensure to remove jumps from the trajectories and/or make m
Dear Mark,
Please find attached a plot showing the RMSD difference. It is for the same
protein.
Even if the same runs are not reproducible, my doubt is whether there can
be such a large variation in the RMSD trend. Which data should I rely on
then, it is giving me a hard time.
I'll be grateful i
Hi,
This is quite normal.
http://www.gromacs.org/Documentation/Terminology/Reproducibility. You
should see a similar range of variation in the trajectories produced in the
two versions that are incompletely sampling the same ensemble, but one can
say very little about two single observed trajector
Dear all,
I have tried running the same protein in the two versions of gromacs 4.6.5
and 5.0.4. Now, both the runs are producing entirely different results.
The results till equilibration are same.
After the run however, there is a total change in the production results. I
have used the same mdp
