Energy analysis with PBSA

[thepoole]

When using the pytraj.esander for pbsa calculations (i.e., igb=10, or with mm_options, ipb>0), the second time it runs there is a memory allocation error leading to a total crash.

I provide here a minimum example using the test trajectory.

`import pytraj as pt
from pytraj.testing import get_fn
import sander

Sander options

options = sander.gas_input(8)
options.igb = 0
options.ipb = 2

Example trajectory

fn, tn = get_fn('ala3')
traj = pt.Trajectory(fn, tn)

execution using mm_options

first=pt.esander(traj=traj, mm_options=options)
second=pt.esander(traj=traj, mm_options=options)

alternative execution using igb=10

first=pt.esander(traj=traj, igb=10)
second=pt.esander(traj=traj, igb=10)`

[hainm]

Thanks @thepoole for your report.

[hainm]

hi @thepoole
I already replied to you in the maillist but this is for the record:

Oh you need a proper prmtop file for that. So you need to prepare it via Leap

Here is an example (I have not validated the result yet, just want to make sure the code runnable)

In [1]: import pytraj as pt

In [3]: traj = pt.iterload("./Tc5b.crd", "Tc5b.prmtop")

In [4]: pt.esander(traj, igb=10) # or: pt.esander(traj, prmtop='Tc5b.prmtop', igb=10)

The data is in here: https://github.com/Amber-MD/pytraj/tree/master/tests/data