[gmx-users] Annealing of shell polarizable water model

[David van der Spoel]

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
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se