Re: AMBER: Temperature fluctuation with Langevin Temperature control

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Sun, 27 Aug 2006 18:07:07 -0300

Gobind Singh Bisht wrote:
> Dear amber users,
> I'm trying to run my simulations at a constant
> temprature using the Lamgevin temperature control. But there are large
> temprature fluctuations (rms 4K). Since I am simulating a small piece of
> DNA
> (42 bp) with implicit solvation I'm equillibrating for only 20ps (with
> delta
> T= 4K). Could that be the reason for the temp fluctuation? Why is there a
> temp fluctuation at all when i specify a target temp. Can someone explain
> me. sry but i'm new to MD and AMBER.
> thanx in advance
>
Gobind,
Why do you think 4K is too much of a fluctuation ?

I think you need to understand the langevin thermostat a bit better
before you can say that 4 K is too much, too little or just right.

Adrian 


-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
============================================================================
To announce that there must be no criticism of the president,
or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
   --  Theodore Roosevelt
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Aug 30 2006 - 06:07:06 PDT
Custom Search