Bug in AMBER patch: passing PBCs with truncated octahedron

[GiovanniBussi]

See this post.

I want to make sure that @dvdesolve is aware of this, since he's the one who did most of the tests (and wrote the pmemd patch).

The proposed solution is to change these lines:

+      plumed_box(1,1) = sqrt(1.0/3.0)*pbc_box(1)
+      plumed_box(2,1) = sqrt(1.0/3.0)*pbc_box(1)
+      plumed_box(3,1) = sqrt(1.0/3.0)*pbc_box(1)
+      plumed_box(1,2) = -sqrt(1.0/3.0)*pbc_box(1)
+      plumed_box(2,2) = -sqrt(1.0/3.0)*pbc_box(1)
+      plumed_box(3,2) = sqrt(1.0/3.0)*pbc_box(1)
+      plumed_box(1,3) = sqrt(1.0/3.0)*pbc_box(1)
+      plumed_box(2,3) = -sqrt(1.0/3.0)*pbc_box(1)
+      plumed_box(3,3) = -sqrt(1.0/3.0)*pbc_box(1)

to:

+      plumed_box(1,1) = pbc_box(1)
+      plumed_box(2,1) = 0.0
+      plumed_box(3,1) = 0.0
+      plumed_box(1,2) = -pbc_box(1)/3.0
+      plumed_box(2,2) = sqrt(8.0/9.0)*pbc_box(1)
+      plumed_box(3,2) = 0.0
+      plumed_box(1,3) = -pbc_box(1)/3.0
+      plumed_box(2,3) = -sqrt(2.0/9.0)*pbc_box(1)
+      plumed_box(3,3) = sqrt(2.0/3.0)*pbc_box(1)

If this is confirmed as a correct fix, the change should be implemented:

• in PMEMD and SANDER (perhaps @dvdesolve could do it)
• in the plumed patch for PMEMD18 - as a bug fix (I can take care of this)

[dvdesolve]

Yep, I've seen messages in plumed-users group. Do we have simplest test case?

[dvdesolve]

I'll raise an issue on AMBER's GitLab too

[GiovanniBussi]

Do we have simplest test case?

The user uploaded a setup, but I cannot run it (don't have amber installed). Should be easy to try. Thanks!

[dvdesolve]

we've merged proposed fix into main Amber source

[dvdesolve]

Updates for Amber20 already released on ambermd.org. So I think you can merge this too

[GiovanniBussi]

(Added notes)
Truncated octahedron Amber.pdf