Feature request: separate alignment and rmsd

[gbowman]

I got a feature request for adding the ability to specify one set of atom indices for alignment and one for the rmsd calculation. Thought I'd put it out here to see if anyone else agrees this would be a useful feature.

[leeping]

Hi Greg,

I think this is already a feature. Not sure how you currently use it (previously it was a part of LPRMSD). Robert might know better than me.

• Lee-Ping

[kyleabeauchamp]

So do you want this as a general trajectory analysis tool or for MSM clustering.

Regardless, this feature should be in MDTraj.

On Wed, Apr 2, 2014 at 2:49 PM, Lee-Ping [email protected] wrote:

Hi Greg,

I think this is already a feature. Not sure how you currently use it (previously it was a part of LPRMSD). Robert might know better than me.

• Lee-Ping

Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/399#issuecomment-39368599 .

[rmcgibbo]

A couple people asked about this at the OpenMM/MSMBuilder workshop this week as well.

On Wed, Apr 2, 2014 at 11:53 AM, kyleabeauchamp [email protected]:

So do you want this as a general trajectory analysis tool or for MSM clustering.

Regardless, this feature should be in MDTraj.

On Wed, Apr 2, 2014 at 2:49 PM, Lee-Ping [email protected] wrote:

Hi Greg,

I think this is already a feature. Not sure how you currently use it (previously it was a part of LPRMSD). Robert might know better than me.

• Lee-Ping

Reply to this email directly or view it on GitHub< https://github.com/SimTk/msmbuilder/issues/399#issuecomment-39368599>

.

Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/399#issuecomment-39369144 .

[dvanatta]

+1 Would be great if this worked with MDTraj in 2.8, I'm still using 2.7 just so I can do the separate alignment and rmsd using lprmsd.