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" <[EMAIL PROTECTED]> 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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