Skip to content

Commit 927264e

Browse files
committed
update user FAQs about eigenvalue warnings
1 parent 4e389a2 commit 927264e

1 file changed

Lines changed: 5 additions & 4 deletions

File tree

docs/faq.rst

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,10 @@
11
Frequently asked questions
22
==============================
33

4-
Why do I get ``nan`` or complex number result?
4+
Why do I get a ``WARNING`` about invalid eigenvalues?
55
--------------------------------------------------
66

7-
Try increasing the sampling time. This is especially true for residue level.
8-
For example in a lysozyme system, residue level we have largest force and torque covariance matrices because at this level we have the largest number of beads (which is equal to the number of resides) compared to the molecule level (3 beads) and UA level (~10 beads per amino acid).
9-
So insufficient sampling might introduce noise and cause matrix elements to deviate to values that would not reflect the uncorrelated nature of force-force covariance of distantly positioned residues.
7+
Insufficient sampling might introduce noise and cause matrix elements to deviate to values that would not reflect the uncorrelated nature of force-force covariance of distantly positioned residues.Try increasing the sampling time. This is especially true at the residue level.
8+
9+
For example in a lysozyme system, the residue level contains the largest force and torque covariance matrices because at this level we have the largest number of beads (which is equal to the number of residues in a protein) compared to the molecule level (3 beads) and united-atom level (~10 beads per amino acid).
10+

0 commit comments

Comments
 (0)