My system:
4713 protein atoms
14925 water molecules
Bonds to hydrogen constrained in protein
Rigid (TIP3P water)
Data previously given to temperature selector:
5000 protein atoms
15000 water molecules
Bonds to hydrogen constrained in protein
Rigid water.
Desired acceptance rate .22
Low temp 270 K
High temp 310 K
Temperature ladder for what was entered previously:
270.00, 271.24, 272.48, 273.72, 274.97, 276.23, 277.49, 278.75, 280.02, 281.30, 282.58, 283.86, 285.15, 286.44, 287.74, 289.04, 290.35, 291.66, 292.98, 294.30, 295.62, 296.95, 298.29, 299.63, 300.98, 302.33, 303.68, 305.04, 306.41, 307.78, 309.15, 310.53
(102433 predicted degrees of freedom)
Temperature ladder from entering correct data:
270.00, 271.24, 272.49, 273.74, 275.00, 276.26, 277.52, 278.79, 280.07, 281.34, 282.63, 283.92, 285.21, 286.51, 287.81, 289.12, 290.43, 291.75, 293.07, 294.39, 295.72, 297.06, 298.40, 299.74, 301.09, 302.45, 303.81, 305.17, 306.54, 307.86, 309.23, 310.62
(101269 predicted degrees of freedom)
Does it seem plausible that this is the cause of the issues? There doesn't seem to be much of a difference between these temperature distribution.
Chris Thiebaut
Graduate Student
Purdue University
----- Original Message -----
From: "Daniel Roe" <daniel.r.roe.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Wednesday, April 9, 2014 1:27:10 PM
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
On Wed, Apr 9, 2014 at 11:20 AM, Jason Swails <jason.swails.gmail.com> wrote:
> That said, I've never seen the temperature range from the REMD
> temperature generator website be so far off before. You should look
> into the source of the degrees-of-freedom discrepancy you described
> earlier. The DOF has a _direct_ effect on replica spacing (it's
> actually additional DOF that requires finer spacing, not additional
> particles, per se).
This I think is the real issue here. The fact that your exchange
acceptances are so high from the start indicates to me that your
replica spacing is too close for your desired exchange acceptance of
22%. If you provided complete details of your system (# atoms, #
waters, etc) and the input you gave to the T-REMD generator we might
be better able to help.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Apr 09 2014 - 11:30:03 PDT
