Re: rmsd calculation in namd

From: Niklaus Johner (nij2003_at_med.cornell.edu)
Date: Fri Sep 07 2012 - 15:53:16 CDT

• Next message: Marc Gordon: "Re: scnb value to prevent VDWs scaling"
• Previous message: Aron Broom: "Re: question about "useflexiblecell' command in NAMD operation"
• Maybe in reply to: Giacomo Fiorin: "Re: rmsd calculation in namd"
• Next in thread: Guanglei Cui: "Re: rmsd calculation in namd"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi,

You can use the PLUMED plugin to do this (http://www.plumed-code.org/). But to do so you'll have to recompile namd with the plugin.

Best,

Niklaus

Niklaus Johner
Weill Cornell Medical College
Harel Weinstein Lab
Department of Physiology and Biophysics
1300 York Avenue, Room D-501
New York, NY 10065

On Sep 7, 2012, at 3:57 PM, Guanglei Cui wrote:

Hi everyone,

can someone let me know if it's possible to define the rmsd collective
variable such that the overlay and rmsd calculation are done on
separate sets of atoms? Thanks very much.

Regards,
Guanglei

• Next message: Marc Gordon: "Re: scnb value to prevent VDWs scaling"
• Previous message: Aron Broom: "Re: question about "useflexiblecell' command in NAMD operation"
• Maybe in reply to: Giacomo Fiorin: "Re: rmsd calculation in namd"
• Next in thread: Guanglei Cui: "Re: rmsd calculation in namd"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:02 CST