Natalie,
With that cppp input you should find in
the execution directory a file traj.axsf
with the 50 (nframes) frames in the animated XSF format (the
default format). The generated PDB is only one frame, likely
the last.
You can read the animated XSF file with VMD
either with "new molecule" or with "load data into molecule"
after reading the PDB with "new molecule".
Giovanni
2016-06-03 18:51 GMT+02:00 Natalie Paige Schieber <
[email protected]>:
> Hello all,
>
> I am having trouble producing a full trajectory to be visualized in VMD
> using car-parrinello molecular dynamics. I am attempting to perform a
> car-parrinello molecular dynamics run on a crystalline benzene system and
> convert the resulting trajectory to a .pdb for visualization. I am not
> receiveing any errors in either the md run or the cppp.x run but the .pdb
> that is output by cppp.x only has a single frame, not the 60 frames that I
> would like. I have attached my input below, excluding the position
> portions, any help would be appreciated!
>
> prefix = 'BNZtsest' ,
> fileout = 'traj' ,
> ldynamics = '.true' ,
> lrotation = '.false' ,
> lpdb = '.true',
> nframes = 50 ,
> atomic_number(1) = 1, atomic_number(2) = 12 ,
> ndr = 50 ,
> lpdb = '.true' ,
>
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