[gmx-users]Simulated annealing
JMandumpal
jesbman at rediffmail.com
Tue Oct 28 05:30:36 CET 2008
Dear Xavier and Jochen,
Thank you for the suggestions: it works well now.
Jes.
On Mon, 27 Oct 2008 Xavier Periole wrote :
>On 27 Oct 2008 06:36:09 -0000
> "JMandumpal" <jesbman at rediffmail.com> 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
>in what follows you have commented out the temperature coupling details.
>I have never used SA but this for sure will not help the program controling
>the temperature! Put these back on should help! :))
>>; 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
>>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.
>>
>>
>>
>>
>>
>>
>>
>
>-----------------------------------------------------
>XAvier Periole - PhD
>
>- Molecular Dynamics Group -
>NMR and Computation
>University of Groningen
>The Netherlands
>-----------------------------------------------------
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