New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

improve documentation of density_from_Universe() #1726

Closed
KyleStiers opened this Issue Dec 7, 2017 · 4 comments

Comments

Projects
None yet
2 participants
@KyleStiers

KyleStiers commented Dec 7, 2017

In the documentation for density_from_Universe() it states:

An input trajectory must

  1. have been centered on the protein of interest;
  2. have all molecules made whole that have been broken across periodic boundaries;
  3. have the solvent molecules remapped so that they are closest to the solute (this is important when using funky unit cells such as a dodecahedron or a truncated octahedron).

In gromacs I've used trjconv to correct my dodecahedron cell for PBC,rotation, and translation, is this what is described as 'remapping'? If not could someone elaborate and update the documentation to reflect a bit more clearly on what is entailed in the remapping?

Thanks!

@orbeckst

This comment has been minimized.

Show comment
Hide comment
@orbeckst

orbeckst Dec 8, 2017

Member

Yes, gmx trjconv -pbc mol -center -ur and then gmx trjconv -fit is exactly what is meant by this statement.

Member

orbeckst commented Dec 8, 2017

Yes, gmx trjconv -pbc mol -center -ur and then gmx trjconv -fit is exactly what is meant by this statement.

@KyleStiers

This comment has been minimized.

Show comment
Hide comment
@KyleStiers

KyleStiers Dec 8, 2017

Great! Thanks. I'd recommend a quick mention of that in the documentation just for to clarify for people.

KyleStiers commented Dec 8, 2017

Great! Thanks. I'd recommend a quick mention of that in the documentation just for to clarify for people.

@KyleStiers KyleStiers closed this Dec 8, 2017

@orbeckst

This comment has been minimized.

Show comment
Hide comment
@orbeckst

orbeckst Dec 8, 2017

Member

Update docs

Member

orbeckst commented Dec 8, 2017

Update docs

@orbeckst orbeckst reopened this Dec 8, 2017

@orbeckst orbeckst added Component-Docs and removed question labels Dec 8, 2017

@orbeckst orbeckst added this to the 1.0 milestone Dec 19, 2017

@orbeckst

This comment has been minimized.

Show comment
Hide comment
@orbeckst

orbeckst Dec 19, 2017

Member

See also #1175

Member

orbeckst commented Dec 19, 2017

See also #1175

@orbeckst orbeckst changed the title from Question on documentation of density_from_Universe() to improve documentation of density_from_Universe() Dec 19, 2017

@orbeckst orbeckst self-assigned this Mar 27, 2018

@orbeckst orbeckst referenced this issue Mar 27, 2018

Merged

Doc fixes #1843

2 of 4 tasks complete

@jbarnoud jbarnoud closed this in d91dd3c Mar 28, 2018

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment