[gmx-users] How to use the simulated annealing porotocal of gromacs 3.3?

SUN, Jian sunjian.nku at gmail.com
Tue May 30 12:38:57 CEST 2006

Dear all,

I am trying to use the simulated annealing porotocal of gromacs 3.3
(single precision) to find the global energy minimization of a protein
in a water box.

I set the mdp file as follow:
title                    = Simulation
; Preprocessor - specify a full path if necessary.
cpp                      = cpp
include                  =
define                   =

integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.001
nsteps                   = 1000000	;1000ps
; For exact run continuation or redoing part of a run
init_step                = 0
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                =

; Type of annealing for each temperature group (no/single/periodic)
annealing                = periodic
; Number of time points to use for specifying annealing in each group
annealing_npoints        = 4
; List of times at the annealing points for each group
annealing_time           = 0 2 8 14
; Temp. at each annealing point, for each group.
annealing_temp           = 270 270 330 270

gen_vel                  = yes
gen_temp                 = 270
gen_seed                 = 173529
constraints              = all-bonds

constrain_algorithm	 = lincs
linvd_order		 = 4

but the run procedure kept on crashing.
I checked the trr file and log file,  and found the energy(potential
energy and total energy) kept on increasing in spite of the temperture
is fluctuating between 270K and 330K.  Why?

Should I set some parameters for constant pressure?

I would be very grateful if you can give me some suggestion.


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