[gmx-users] Simulated Annealing

[Shang-Te Danny Hsu]

Hi there,

I am trying to perform Simulated Annealing protocol by GROMACS3.0. I 
simply adopted the runfile *.mdp from my previous simulation at constant 
temperature by adding:

; Simulated Annealing
annealing = yes
zero_temp_time = -1000

Negative zero_temp_time is to heat up the system. Then the system blows 
up at step0 with lots of bond length violation. The system has been 
first energy minimized and released for dynamics for 100ps in water. 
Should be more or less stable. What are the possibilities to fix this 
problem?

[here is the *.mdp file]
========================

title               =  SA_test
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
tinit               =  0.0
dt                  =  0.001    ; ps !
nsteps              =  20000   ; total 20 ps.
nstcomm             =  1
nstxout             =  5000
nstvout             =  5000
nstfout             =  0
nstxtcout           =  500
xtc_precision       =  1000
nstlog              =  125
nstenergy           =  125
nstlist             =  10
rlist               =  0.8
coulombtype         =  generalized-reaction-field
rcoulomb            =  1.4
rvdw                =  1.4
epsilon_r           =  54.0
; Temperature coupling is on in two groups
Tcoupl              =  Berendsen
tc-grps             =  Protein    SOL
tau_t               =  0.1        0.1
ref_t               =  300        300
; Simulated Annealing
annealing           =  yes
zero_temp_time      =  -1000
; Energy monitoring
energygrps          =  Protein  SOL
; Pressure coupling is not on
Pcoupl              =  Berendsen
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529
-- 
Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl