[CP2K:7144] Re: Choosing a structure from equilibrium QM/MM trajectory for the next Metadynamics run

tarak karmakar tarak... at gmail.com
Wed Nov 11 07:03:21 UTC 2015

Dear Marcella,
Thanks for the reply.
In the latest metadynamics run, I have selected a frame from the .dcd
trajectory after wrapping the coordinates using the pbc plugin in VMD.
Things are going well as of now.


On Tue, Nov 10, 2015 at 7:21 PM, Marcella Iannuzzi <marci... at gmail.com>

> 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
> plug-in.
> Marcella
> 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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