On Wed, Nov 14, 2012 at 4:54 PM, Kepa K. Burusco <kekoburgo.yahoo.es> wrote:
>
> Unfortunately, I am not yet an expert in the code so, my question is,
> would it be any problem to compute the total energy (and the single
> contributions: BOND, ANGLE, DIHED, VDW, EELEC, 1-4EL, 1-4NB) by using the
> imin=5 option rather than splitting the trajectory and running 1-step MD
> for every single snapshot?
>
One gotcha here. For an FEP- or MBAR-type of calculation that depends on
energies for each conformation for each topology file, you will still need
to re-run sander using imin=5 even for the original topology file that was
used to generate that trajectory.
You cannot simply use the energies in the original molecular dynamics mdout
file*. And here is why:
The (simplified) workflow inside the molecular dynamics code is:
1) calculate forces and energies
2) propagate coordinates using newton's laws of motion
3) update velocities
4) if any printing needs to be done (e.g., mdout, mdcrd, etc.), do this now
5) go back to 1)
As a result, the printed energies and coordinates are separated by an
effective time step, since the coordinates used to calculate the printed
energies (and forces) were the coordinates *prior* to the update in step 2).
Good luck,
Jason
*You can avoid this by setting ntpr=1 and taking the energies from the step
immediately *after* coordinates are printed. But this leads to potentially
huge mdout files.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Nov 15 2012 - 08:30:03 PST
