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msmbuilder / msmbuilder-legacy

Legacy release of MSMBuilder
http://msmbuilder.org
GNU General Public License v2.0
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Feature request: separate alignment and rmsd #399

Open gbowman opened 10 years ago

gbowman commented 10 years ago

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 commented 10 years ago

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.

kyleabeauchamp commented 10 years ago

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 notifications@github.com 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 commented 10 years ago

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 notifications@github.comwrote:

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 notifications@github.com 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 commented 10 years ago

+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.