[gmx-users] binding sites with MD

Albert mailmd2011 at gmail.com
Sat May 24 22:08:23 CEST 2014

this plug-in looks interesting.

However, as far as I saw from the tutorial that even we run simulation 
from Gromacs, this plugin can only import NAMD psf and DCD to analysis. 
That's  a headache issue. Can you improve this vmd plugin so that it can 
also read Gromacs format files directly?


On 05/24/2014 07:02 PM, Tom Dodson wrote:
> Nidhi,
> You might be interested in this tool:http://prody.csb.pitt.edu/drugui/
> Here are slide from a talk about the method:
> http://mmbios.org/images/workshops/HandsOn2014/Lecture3.pdf
> And here is a tutorial:
> http://prody.csb.pitt.edu/tutorials/drugui_tutorial/drugui_tutorial.pdf
> I am sure that you could use GROMACS to do the simulated annealing step
> instead of NAMD.
> Tom

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