selecting coordinates from .dcd for next step of QM/MM simulation

tarak karmakar tarak... at gmail.com
Fri Sep 18 11:21:53 CEST 2015


Dear All,
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 method.
My question is,
How do I select a frame from the 10 ps .dcd trajectory that can be used in
the meta.inp file for next step calculations?

DCD file does not wrap the coordinates, and thus the box information is
lost (few molecules are out of the box). 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,
Tarak
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