[gmx-users] Annealing of shell polarizable water model

[Ivan Gladich]

Dear all,
          I would like to heat, very slowly, a ice box of 1796 SWM4-NDP 
water.
This kind of water has 4 sites plus a shell and I am using a small time 
step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns.
To do that  I used a linear annealing from 0 to 160 K.

The simulation runs without problem but I cannot reach the desire 
temperature.
In other words, if I look my md.log file I can see the ref_t that linear 
increase from 0 to 160 K in 1 ns but the system temperature seems to do 
not follow the thermostate temperature.
If I plot the temperature obtained from g_energy, the temperature of the 
system remains constant at ~36 K.
I attach also my temperature profile up to 600ps. Due to the small time 
step the simulation takes a bit of time but it is clear that the 
temperature remain constant


I have tried to find in the mail list some similar problem without 
success...
Here below I report my grompp. Maybe I missed something.
Thank in advance for any suggestions.
Ivan
#########################################3
; VARIOUS PREPROCESSING OPTIONS
title                    = Ice SWM4-NDP
cpp                      = /usr/bin/cpp
include                  =
define                   =

; RUN CONTROL PARAMETERS
integrator               =  md
dt                       = 0.0001
nsteps                   = 14000000

; 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                =

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint            = 10000
; Output frequency for energies to log file and energy file
nstlog                   = 5000
nstenergy                = 1000
; Output frequency and precision for xtc file
nstxtcout                = 10000
xtc-precision            = 1000

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 5
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc                      = xyz
; nblist cut-off
rlist                    = 1.1
;domain-decomposition     =

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 1.1
; Method for doing Van der Waals
vdw-type                 = Cut-off
rvdw-switch              = 0
rvdw                     = 1.1

; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
optimize_fft             = no

;OPTIONS FOR ANNELING
annealing = single
annealing_npoints = 2
annealing_time = 0 1000
annealing_temp = 0 160

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = Nose-hoover
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1
ref_t                    = 160.00
; Pressure coupling
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    =  2.0
compressibility     =  4.5E-5
ref_p                     =  0.0
; Random seed for Andersen thermostat
andersen_seed            = 815131

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = yes
gen_temp                 = 0
gen_seed                 = 1993

;CONSTRAINTS
constraints              = hbonds
constraint_algorithm     = LINCS

-- 
------
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-----

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