When running normal modes on a structure, unless one thread is used, the energy will not be the same as the previous minimization
As noted above:
No idea who to assign to.
When I minimize a structure, I can get down to the force max being <0.01
Low-Memory BFGS Minimizer converged to Fmax < 0.01 in 6839 steps
Potential Energy = -5.12340607768673e+03
Maximum force = 6.68907856457542e-03 on atom 3029
Norm of force = 2.19978176343026e-03
kJ/nm. However, when I try to perform a normal mode analysis, it
complains that the maximum energy is >30 kJ/mn.
Non-cutoff electrostatics used, forcing full Hessian format.
Allocating Hessian memory...
Maximum force: 3.91984e+01
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.
Fix was to run with -nt 1, and then the maximum force was exactly the same.
#3 Updated by Mark Abraham about 4 years ago
David van der Spoel wrote:
Is there a test set?
(I have master-branch machinery to add lightweight versions of such tests mostly ready, but not yet fit for routine use. Some of Teemu's more recent stuff with options parsing will be very useful.)
I assume this is not done using the .gro output file from the minimization?
#13 Updated by Berk Hess about 4 years ago
- Status changed from New to Fix uploaded
- Assignee changed from Mark Abraham to Berk Hess
NM parallelizes over gradient components (no particle/domain decomposition). This means every MPI rank does a separate force calculation.
However, PME was still initialized (on every rank) with a parallel setup.
I assume 4.5 was also affected by this. I uploaded a proper fix.