[gmx-users]Simulated annealing
Jochen Hub
jhub at gwdg.de
Mon Oct 27 08:45:47 CET 2008
JMandumpal wrote:
>
> Dear GROMACS users,
>
> I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water:
>
> the task:
>
> I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps time ( fast cooling). For that I used the following script:
>
> title = Water annealing simulation
> cpp = /usr/bin/cpp
> ; RUN CONTROL PARAMETERS
> integrator = md
> ; Start time and timestep in ps
> dt = 0.001; 1fs
> nsteps = 100000 ; 1ps
> ; For exact run continuation or redoing part of a run
> init_step = 0
> ; number of steps for center of mass motion removal
> nstcomm = 1
> ; group(s) for center of mass motion removal
> comm-grps = SOL
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 10000 ; 10ps
> nstvout = 10000 ; 10ps
> nstfout = 0
> ; Checkpointing helps you continue after crashes
> nstcheckpoint = 100
> ; Output frequency for energies to log file and energy file
> nstlog = 0
> nstenergy = 1000 ; 1ps
> ; Output frequency and precision for xtc file
> ;nstxtcout = 0
> ;xtc-precision = 1000
> ; select multiple groups. By default all atoms will be written.
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist = 10
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions:
> pbc = xyz
> ; nblist cut-off
> rlist = 1.0
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = pme
> rcoulomb = 1.0
> ewald_rtol = 1.0e-5 ; since erfc(sigma*rcutoff)=ewald_rtol
> optimize_fft = yes
> ; Relative dielectric constant for the medium
> epsilon_r = 1 ; for water
> ; Method for doing Van der Waals
> vdw-type = cut-off
> rvdw = 1.0
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12 ; check for the range 0.1 to 0.15
> ; EWALD/PME/PPPM parameters
> pme_order = 4
> ewald_geometry = 3d
> epsilon_surface = 0
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> ;Tcoupl = berendsen
> ; Groups to couple separately
> ;tc-grps = system
> ; Time constant (ps) and reference temperature (K)
> ;tau-t = 0.1
> ;ref-t = 360
> ; simulated anealing
> annealing = single
> annealing_npoints = 2
> annealing_time = 0 0
^^^^^^^
I think this should be
annealing_time = 0 100
in your case, right?
Jochen
> annealing_temp = 360 0
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = yes
> gen-temp = 360
> gen-seed = 173529
> ; OPTIONS FOR BONDS
> constraints = all-bonds
> constraint_algorithm = shake
> shake_tol = 0.0001
> morse = no
> -----------------------------------------------------------------------
>
> Problem:
>
> Having done the simulations, the output shows ( ener.edr , Temperature) a high temperature value around 850K. Clearly I did something wrong in my parameter file.
>
> -------------------------------------------------------
> the temperature extracted after the simulations
> -------------------------------------------------------
> s0 legend "Temperature"
> 0.000000 376.058044
> 1.000000 864.033020
> 2.000000 873.607605
> 3.000000 851.308838
> 4.000000 847.223877
> 5.000000 860.511841
> 6.000000 813.547241
> 7.000000 845.261658
> 8.000000 872.090027
> 9.000000 852.079468
> 10.000000 849.152466
> 11.000001 850.055237
> 12.000001 834.468323
> 13.000001 861.107300
> 14.000001 828.380493
> 15.000001 850.166809
> 16.000000 850.382019
> 17.000000 847.214478
> 18.000000 851.201538
> 19.000000 857.533691
> 20.000000 849.760071
> 21.000002 864.907715
> 22.000002 837.307495
> 23.000002 827.407593
> 24.000002 841.464111
> 25.000002 863.330688
> 26.000002 841.096069
> 27.000002 856.469910
> 28.000002 854.449768
> 29.000002 845.534973
> 30.000002 853.421448
> 31.000002 825.198059
> 32.000000 857.317566
> 33.000000 823.510925
> 34.000000 858.875122
> 35.000000 880.710266
> 36.000000 853.692749
> 37.000000 847.079468
> 38.000000 851.004822
> 39.000000 858.750000
> 40.000000 872.787048
> 41.000004 843.033813
> 42.000004 874.984009
> 43.000004 845.272583
> 44.000004 822.993713
> 45.000004 863.116455
> 46.000004 865.640198
> 47.000004 873.489563
> 48.000004 849.170776
> 49.000004 861.631958
> 50.000004 860.999939
> 51.000004 834.341003
> 52.000004 864.601196
> 53.000004 838.268372
> 54.000004 842.860046
> 55.000004 837.590332
> 56.000004 855.985046
> 57.000004 836.168030
> 58.000004 862.147644
> 59.000004 869.183044
> 60.000004 873.057556
> 61.000004 871.051636
> 62.000004 857.647217
> 63.000004 857.834106
> 64.000000 871.380981
> 65.000000 850.045654
> 66.000000 880.142456
> 67.000000 844.183350
> 68.000000 850.980042
> 69.000000 854.431091
> 70.000000 847.898743
> 71.000000 859.750488
> 72.000000 852.219910
> 73.000000 854.833984
> 74.000000 851.676514
> 75.000000 866.519287
> 76.000000 861.120605
> 77.000000 857.873230
> 78.000000 845.287720
> 79.000000 874.603333
> 80.000000 854.244751
> 81.000008 864.049561
> 82.000008 892.515991
> 83.000008 855.164734
> 84.000008 867.054077
> 85.000008 862.560059
> 86.000008 829.368469
> 87.000008 864.729553
> 88.000008 882.954102
> 89.000008 865.048401
> 90.000008 864.581848
> 91.000008 870.596619
> 92.000008 856.474976
> 93.000008 861.473450
> 94.000008 838.902344
> 95.000008 896.907715
> 96.000008 865.042480
> 97.000008 877.761292
> 98.000008 877.356750
> 99.000008 855.421753
> 100.000008 863.720398
> ------------------------------------------------------
>
> Could anyone tell me what changes I should make in the parameter file?
>
>
>
> Many thanks,
> Jes.
>
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> ------------------------------------------------------------------------
>
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--
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
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