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

Marcella Iannuzzi marci... at
Tue Nov 10 13:51:30 UTC 2015

Dear Tarak,

using PBC, the un-wrapped and the wrapped coordinates are equivalent. Hence 
you can use one frame taken from your trajectory to restart the 
calculation. Since the MD is NVT the box is always the same. If you do not 
like the visualisation of the diffusing water molecules, wrap them back 
into the box. If you don't like writing a script for that, use the pbc VMD 


On Monday, November 9, 2015 at 2:32:31 PM UTC+1, tarak wrote:
> 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,
> Tarak
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