From: Jason Swails (jason.swails_at_gmail.com)
Date: Sun Apr 24 2016 - 00:23:50 CDT
How different are the energies? And how long was your simulation run for?
Ideally the energies *should* be identical. However, trajectories are
typically stored in single precision rather than full double precision (and
that's true for the DCD format). This means that coordinates lose
precision a lot faster when read from a trajectory as opposed to a data
source that stores double precision data. If you store the trajectory in a
crappy format, like simple truncated ASCII or PDB, then this scenario
becomes even more pronounced.
Of course there are many other ways that energies can differ by small
amounts as well:
1. The PME grid is set up differently (possible particularly when doing NpT
calculations where the unit cell size changes)
2. If the unit cell dimensions change (i.e., because you are running NpT
calculations), then you have to make sure that the unit cell vectors
applied to every frame is the same as the unit cell vectors for that
particular frame.
#1 is a likely concern (check for electrostatic energy differences). I
would expect #2 to be handled automatically (since DCD files store unit
cell information for each frame), but it's worth checking to make sure.
The trick here is to find some frames where the energy differs, and see
where the energy differs and by how much.
HTH,
Jason
On Sat, Apr 23, 2016 at 10:22 PM, zeynab hoseyni <zmhoseyni_at_gmail.com>
wrote:
> Dear all,
>
> I ran NVT simulation of a nano-tubes in addition to a dimer solvated in
> water. In the namd conf file
> I turned on the wrapAll and wrapWater options. I saw that the nano-tube
> and dimer were so
> much moving around and going out of the simulation box frequently during
> the simulation. Since I already turned
> on the wrap options then sometimes either nano-tube or dimer jump from one
> side to the other side
> of simulation box, depending on which one catching the side wall, not
> suitable for doing some
> calculations. I then decided to unwrap the nano-tube (resname CNT) and
> dimer (resname ARG)
> by following command in vmd:
>
> pbc unwrap -sel "resname CNT or resname ARG" -all
>
> Doing so I calculated the total energy of the wrapped and unwrapped
> trajectories using namd energy
> plugin. I expected they show the same plot of total energy versus time,
> but they show slightly different plots.
>
> Can anyone help on this? In addition to this I don't have a
> clear understanding of what wrapping option
> does in namd or vmd as I see sometimes nano-tube or dimer traverses the
> cell side (one part pass the side
> and one part still in the box) but it isn't wrapped and sometimes it is in
> the similar situations and it would be wrapped..
> Don't know exactly what it does.. Can anyone introduce me some reference
> or tutorial to understand more?
>
> Thanks,
> Zeynab
>
>
-- Jason M. Swails
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