[gmx-users] Annealing of shell polarizable water model

Ivan Gladich ivan.gladich at marge.uochb.cas.cz
Wed Mar 23 09:16:12 CET 2011 

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: ivan.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-----

More information about the gromacs.org_gmx-users mailing list