Previous Thread
Next Thread
Print Thread
Integration with conditional harmonic constraints
#32009 05/30/13 10:41 PM
Joined: Oct 2005
Posts: 206
P
prakash Offline OP
Forum Member
OP Offline
Forum Member
P
Joined: Oct 2005
Posts: 206
I like to apply harmonic constraints on all c-alpha atoms during MD-vacuo, with a condition apply to maintain inter c-alpha atom distance should be less than or equal to certain threshold (eg:9 Angs) during the integration.

Are there any method exist to call harmonic constraints for the above mentioned condition.

Appreciate your help

Thanks



saravana

Re: Integration with conditional harmonic constraints
prakash #32010 05/31/13 12:38 AM
Joined: Sep 2003
Posts: 8,545
Likes: 3
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,545
Likes: 3
Not exactly.

There is CONS HARM BESTFIT, which applies a restraint force for an RMSD best fit to a set of atoms (e.g. Calpha), allowing for translation and rotation; see cons.doc for details. You'd probably have to tune the restraint force to keep the deviations within some threshold value.

You can use multiple restraint sets applied to secondary structure elements or protein domains, but the atom selections should not overlap; a given atom can only be in one harmonic restraint set.


Rick Venable
computational chemist


Moderated by  BRBrooks, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.011s Queries: 18 (0.006s) Memory: 0.8941 MB (Peak: 0.9620 MB) Data Comp: Off Server Time: 2021-05-06 16:41:15 UTC
Valid HTML 5 and Valid CSS