[gmx-users] supervised MD in Gromacs?

Albert mailmd2011 at gmail.com
Tue Dec 8 16:07:11 CET 2015

Thanks for the comments.

In this case, it is probably meaningless to compare the kinetic of two 
ligand based on the time that ligand jump from bulk water into the 
binding pocket.....Neither could one be sure that the final pose is 
close to the crystal structure.....


On 12/08/2015 03:03 PM, Piggot T. wrote:
> Hi Albert,
> A simple script to run:
> 1) a short simulation
> 2) g_dist/gmx distance
> 3) g_analyze/gmx analyze
> 4) decide to continue the simulation from the final coordinates or restart the simulation from the initial coordinates
> should do the trick I think to reproduce the SuMD method given in the first paper you originally linked to. I've not done it myself though.
> Cheers
> Tom

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