AMBER Archive (2009)

Subject: RE: [AMBER] Distance Replica Exchange

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Fri Oct 09 2009 - 09:21:13 CDT

Ok. Thanks Carlos for the information. Obviously, I need to some more reading.

Steve

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of Carlos Simmerling
Sent: Friday, October 09, 2009 9:40 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Distance Replica Exchange

Steve,
this may be implemented in amber11- but I caution that distance REMD samples
"better" only if your particular system has a sampling barrier than can be
described well with a distance. for many complex systems, defining an
appropriate collective variable is a major challenge affecting not only
REMD, but umbrella sampling and other methods. while far from perfect,
temperature REMD requires much less information about the details of the key
barriers.
carlos

On Fri, Oct 9, 2009 at 9:18 AM, Steve Seibold <seibold_at_chemistry.msu.edu>wrote:

>
> Hello
> Does AMBER 10 support "Distance Replica Exchange Method"? I realize that it
> does have, as AMBER 8 & 9, temperature jumps REM.
>
> I have read (though I am NOT an expert) that distance replica exchange
> samples better than temperature REM. Is this something that AMBER 11 might
> come out with if version 10 does not contain this method?
>
> Thanks
> Steve
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber