[gmx-users] Annealing of shell polarizable water model

[Ivan Gladich]

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/
-----