[CP2K-user] Full QM DFT Metadynamics Simulation of water and ATP resulting in a lot of vaccum
marci... at gmail.com
Fri Jan 4 14:18:34 UTC 2019
Dear Raghav Saxena,
Did you run an equilibration MD before starting the metadynamics run?
If yes, did you check the density and the radial distribution function of
the liquid water after equilibration?
Your DFT parameters are not very good. For instance, basis set, PW cutoff,
and convergence criterion could be improved.
On Friday, January 4, 2019 at 11:43:23 AM UTC+1, Raghav wrote:
> Dear all,
> I'm doing *full QM DFT* Meatdynamics simulation with *PBC* of
> liquid water and a Triphosphate molecule. During my 3ps simulation, the
> water molecules in the cubic box are contracting and forming a kind of
> droplet around the triphosphate molecule as can be seen in the attached
> images *initial.tga* and *final.tga*. I don't know why this is happening.
> I have attached my Input file and the snapshot of the first and last point
> of trajectory (initial.tga and final.tga respectively). It's clear from the
> snapshots how water goes from cubic configuration in initial.tga to a drop
> like configuration in final.tga, and because of this I have a lot of vacuum
> in my box.
> Is it because of the collective variable which involves coordination
> number of phosphorus with all QM water oxygen's or It's something else? I
> have also attached my input file for reference.
> I would really appreciate some help. Looking forward for a reply.
> Thank's and Regards,
> Raghav Saxena
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