1) Langvin MD
In results i got one device configuration file and one MD trajectory file. In MD trajectory file I got following results, PFA. can you tell me what does it signify and what does it optimize?
MD does not optimize anything. It generates a number of snapshots drawn from a canonical ensemble. Note that different snapshots of the same MD simulation may yield different results for the same property. That means that a single snapshot from an MD trajectory not may be too meaningful, but it is rather the average over many snapshots that should be considered.
In your case you have simulated only over a very short time span and the system has very likely not had enough time to reach thermal equilibrium. This is the reason why the molecule looks a bit strange.
Please read the tutorial about MD simulations (
www.docs.quantumwise.com/tutorials/md_basics.html) to learn more about how to equilibrate a system.
2) Geometry Optimization
In results i got two device configuration files and when i drag .nc file into stash it generated two device structure there. Then I checked their coordinates and i found that two device structures have different coordinates. Do you think that changed coordinates are geometry optimized one. Also I checked it for only 10 steps, do you think that increasing steps will give much better results.
The first of the two configuration is the initial structure of the device, whereas the second one is the structure after optimizing the geometry, i.e. minimizing the total energy. They should have different coordinates, as the atomic positions change during the optimization. That means the second configuration is the one to use.
In geometry optimization the decisive criteria is not the number of steps but the max. force parameter, which sets the threshold that the optimization stops as soon as the forces on all atoms are below this value. The default value of 0.05 eV/Ang is generally ok, for a very precise optimization it should be decreased, though.
The number of steps is only a parameter that prevents that an optimization simulation runs forever if it for some reason doesn't manage to converge.
In your case, you should check at the end of the log file, if the optimization has converged, i.e. if all forces are below the specified max. force value. There will be a line which informs you about this.
