[gmx-users] Annealing of shell polarizable water model
ivan.gladich at marge.uochb.cas.cz
Tue Mar 22 13:35:44 CET 2011
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?
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....
> 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
>>> In other words, if I look my md.log file I can see the ref_t that
>>> 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
>>> 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
>>> Here below I report my grompp. Maybe I missed something.
>>> Thank in advance for any suggestions.
>>> ; 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 = hbonds
>>> constraint_algorithm = LINCS
Ivan Gladich, Ph.D.
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
e-mail: ivan.gladich at uochb.cas.cz
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