[gmx-users] (no subject)

[Dallas Warren]

In molecular dynamics things move around.

The fact that the molecules aren't in the starting position shows that it
isn't a stable configuration, the interactions between the protein and the
molecules are insufficient to keep them together in that spot.

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 Thu, 28 Mar 2019 at 05:50, saranya <saranyahoney17 at gmail.com> wrote:

> Hi users,
>
>       I have simulated a protein with gas molecules (CO2,NO2 and SO2) for
> 100ns. I have followed the  protein ligand tutorial. I have applied
> position constraints. After equilibrium the gas molecules are at the docked
> position but at the 60ns simulation the gas molecules are far away from the
> protein. I have applied pBC and sure this is not an visualisatuin error.
> How can I rectify this, Kindly give your valuable suggestions in this
> regard.
>
>
>
> --
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
> --
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