Dear Justin,
Dear all
you guessed right.
I am now using a v-rescale thermostate
and it works fine and it also runs in parallel.
Here below the changed part in my grompp with the v-rescale thermostate.
Thanks a lot
Ivan
###################################
;OPTIONS FOR ANNELING
annealing = single
annealing_npoints = 2
annealing_time = 0 1000
annealing_temp = 0 160
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = v-rescale ;Nose-hoover
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 160.00
######################################
On 03/22/2011 01:09 PM, Justin A. Lemkul wrote:
Ivan Gladich wrote:
Dear David
Dear all
I did the serial run with the same topology and grompp: even if the
simulation time is still short (due by the serial run), the
temperature profiles are the same (see attached file).
As further check, I removed the annealing and the temperature rises
to 160 K after ~0.5ps without problem.
So I do not think that it is a problem of the shell polarizability
with the running in parallel.
Could be a problem of the shell polarizability with annealing?
You could test that relatively easily with a simple box of water. The
result would be useful.
Other than that, maybe the thermostat itself is causing the problem?
I always do annealing with a weak coupling method, not Nose-Hoover.
I've had stability problems with unequilibrated systems with N-H. In
principle, it shouldn't matter, but setting tcoupl to Berendsen and/or
V-rescale would be another very useful diagnostic.
-Justin
Thanks again
Ivan
On 03/22/2011 10:45 AM, Ivan Gladich wrote:
Yes, I am running in parallel...
Now I will try to run in serial to see if the problem persist....
Thanks
Ivan
On 03/22/2011 10:00 AM, David van der Spoel wrote:
On 2011-03-22 10.37, Ivan Gladich wrote:
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.
Are you running in parallel? Unfortunately polarizable MD is broken
on more than 1 core. There is a redmine issue for this, and it will
be fixed soon.
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: [email protected]
web page:http://www.molecular.cz/~gladich/
-----
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