AW: is there a method equivalent to conformational flooding in NAMD 2.10

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jan 12 2015 - 00:53:25 CST

Hi,

 

well you are likely caught in a deep minimum, which actually could be the global one aswell, doesn’t it? Either this would explain why nothing happens, or if you think there should be happening something, you’d like to put more energy into the system to actually allow conformational changes and crossing energy barriers. At which temperature did you run this 1µs? I think you could try to run a usual MD at a higher temperature, but not high enough to cause complete unfolding. Another option might be a REMD with lower Tmax to do the same.

 

Also, are you sure that your settings for the aMD were suitable? Maybe you can post them here along with some details about the size of the protein and so someone can share some opinions about it.

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Thomas Evangelidis
Gesendet: Sonntag, 11. Januar 2015 14:44
An: namd-l
Betreff: namd-l: is there a method equivalent to conformational flooding in NAMD 2.10

 

 

Dear NAMD list,

Is there any method in NAMD equivalent to Helmut Grubmuller's Conformational Flooding? I want to open a transporter starting from an intermediate state in which it was crystallized, but I don't know the final state. So far, I have ran a 1 microsecond aMD simulation but nothing happened. I conducted all my simulations with NAMD hence I hesitate migrating to GROMACS.

thanks,
Thomas 

-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===============================================================
Physics is the only real science. The rest are just stamp collecting.
- Ernest Rutherford

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:20:48 CST