[gmx-users] "Re: Shape of the aggregate (Dallas Warren)"

[Dallas Warren]

Did you do this check? That's the only point at which I can see there would
be a difference.
"Other thing to check is whether the first and last atom in the index group
selected when using polystat is the same as the two atoms you selected in
VMD."

Whether coarse grain or all atom will make no difference, as all it is
doing is measuring the distance between two points.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Wed, 9 Oct 2019 at 22:36, Aishwarya Dhar <dhar.aishwarya at gmail.com>
wrote:

> Yes, of course I know that GROMACS measures things in nanometers and VMD
> uses Angstroms.
>
> Basically it is in coarse grain representation.  In general since the
> aggregate consist of all the beads. I have taken the entire pdb of the
> aggregate as in input which should take the end to end distance.
>
> Do you think that it the problem of Coarse Grain bead?
> Or is there anything I am missing?
>
>
>
> Aishwarya
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