Choosing a structure from equilibrium QM/MM trajectory for the next Metadynamics run

tarak karmakar tarak... at
Mon Nov 9 13:32:29 UTC 2015

Dear All,
Sorry for re-posting the same question that I had posted couple of months
back but did not get a reply.

I have finished 10 ps of QM/MM equilibration of my protein-ligand complex
in NVT ensemble. Now, I need to study the chemical reaction using
metadynamics simulation.

My question is,
How do I select a frame from the 10 ps .dcd trajectory that can be used in
the metadynamics simulation, I need to perform next?

DCD file does not wrap the coordinates, and thus the box information is
lost. When I visualize the trajectoy in VMD (.dcd and .psf) water molecules
(surface) are floating out of the simulations box. I realize that this is
because of the un-wrapped coordinates. In that case, selecting a frame from
VMD (after loading the .dcd and .psf), I think, is not a good idea.

Could anyone suggest a protocol of how to extract frames from the
trajectory that can be used in the next set of simulations?
Do I need to wrap the coordinates in vmd and then save the .pdb files?

Suggestions will be immensely appreciated.

Thanks and regards,
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