Dear David Dear allI 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? 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: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.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.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 linearincrease 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 thesystem 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.glad...@uochb.cas.cz web page:http://www.molecular.cz/~gladich/ -----
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