[gmx-users] Shape of the aggregate

Dallas Warren dallas.warren at monash.edu
Mon Oct 7 22:45:27 CEST 2019


First thing is that GROMACS measures things in nanometers, whereas VMD uses
Angstroms.

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.

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 Tue, 8 Oct 2019 at 02:21, Aishwarya Dhar <dhar.aishwarya at gmail.com>
wrote:

> Hi
> I am trying to calculate the shape of an aggregate which is cylindrical in
> shape.
> I have used the command
> gmx polystat -f aggregate.pdb -s aggregate.tpr -o poly.xvg
>
> The eigen values  from gmx polystat  of the aggregate  for a particular
> frame are  3.3566 0.8837 0.7660 but using VMD the distance between the
> extreme ends of the rods are  114.1 29.5 27.8 in that particular frame
> Could you tell me what am I missing?
>
> Thank you
>
> AIshwarya
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