<P>
Dear Xavier and Jochen,<BR>
<BR>
Thank you for the suggestions: it works well now.<BR>
<BR>
Jes.<BR>
<BR>
<BR>
On Mon, 27 Oct 2008 Xavier Periole wrote :<BR>
>On 27 Oct 2008 06:36:09 -0000<BR>
> "JMandumpal" <jesbman@rediffmail.com> wrote:<BR>
>> Dear GROMACS users,<BR>
>><BR>
>>I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water:<BR>
>><BR>
>>the task:<BR>
>><BR>
>>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:<BR>
>><BR>
>>title = Water annealing simulation<BR>
>>cpp = /usr/bin/cpp<BR>
>>; RUN CONTROL PARAMETERS<BR>
>>integrator = md<BR>
>>; Start time and timestep in ps<BR>
>>dt = 0.001; 1fs<BR>
>>nsteps = 100000 ; 1ps<BR>
>>; For exact run continuation or redoing part of a run<BR>
>>init_step = 0<BR>
>>; number of steps for center of mass motion removal<BR>
>>nstcomm = 1<BR>
>>; group(s) for center of mass motion removal<BR>
>>comm-grps = SOL<BR>
>>; OUTPUT CONTROL OPTIONS<BR>
>>; Output frequency for coords (x), velocities (v) and forces (f)<BR>
>>nstxout = 10000 ; 10ps<BR>
>>nstvout = 10000 ; 10ps<BR>
>>nstfout = 0<BR>
>>; Checkpointing helps you continue after crashes<BR>
>>nstcheckpoint = 100<BR>
>>; Output frequency for energies to log file and energy file<BR>
>>nstlog = 0<BR>
>>nstenergy = 1000 ; 1ps<BR>
>>; Output frequency and precision for xtc file<BR>
>>;nstxtcout = 0<BR>
>>;xtc-precision = 1000<BR>
>>; select multiple groups. By default all atoms will be written.<BR>
>>; NEIGHBORSEARCHING PARAMETERS<BR>
>>nstlist = 10<BR>
>>; ns algorithm (simple or grid)<BR>
>>ns_type = grid<BR>
>>; Periodic boundary conditions:<BR>
>>pbc = xyz<BR>
>>; nblist cut-off<BR>
>>rlist = 1.0<BR>
>>; OPTIONS FOR ELECTROSTATICS AND VDW<BR>
>>; Method for doing electrostatics<BR>
>>coulombtype = pme<BR>
>>rcoulomb = 1.0<BR>
>>ewald_rtol = 1.0e-5 ; since erfc(sigma*rcutoff)=ewald_rtol<BR>
>>optimize_fft = yes<BR>
>>; Relative dielectric constant for the medium<BR>
>>epsilon_r = 1 ; for water<BR>
>>; Method for doing Van der Waals<BR>
>>vdw-type = cut-off<BR>
>>rvdw = 1.0<BR>
>>; Spacing for the PME/PPPM FFT grid<BR>
>>fourierspacing = 0.12 ; check for the range 0.1 to 0.15<BR>
>>; EWALD/PME/PPPM parameters<BR>
>>pme_order = 4<BR>
>>ewald_geometry = 3d<BR>
>>epsilon_surface = 0<BR>
>>; OPTIONS FOR WEAK COUPLING ALGORITHMS<BR>
>>; OPTIONS FOR WEAK COUPLING ALGORITHMS<BR>
>in what follows you have commented out the temperature coupling details.<BR>
>I have never used SA but this for sure will not help the program controling<BR>
>the temperature! Put these back on should help! :))<BR>
>>; Temperature coupling<BR>
>>;Tcoupl = berendsen<BR>
>>; Groups to couple separately<BR>
>>;tc-grps = system<BR>
>>; Time constant (ps) and reference temperature (K)<BR>
>>;tau-t = 0.1<BR>
>>;ref-t = 360<BR>
>>; simulated anealing<BR>
>>annealing = single<BR>
>>annealing_npoints = 2<BR>
>>annealing_time = 0 0<BR>
>>annealing_temp = 360 0<BR>
>>; GENERATE VELOCITIES FOR STARTUP RUN<BR>
>>gen_vel = yes<BR>
>>gen-temp = 360<BR>
>>gen-seed = 173529<BR>
>>; OPTIONS FOR BONDS<BR>
>>constraints = all-bonds<BR>
>>constraint_algorithm = shake<BR>
>>shake_tol = 0.0001<BR>
>>morse = no<BR>
>> -----------------------------------------------------------------------<BR>
>><BR>
>>Problem:<BR>
>><BR>
>>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. <BR>
>>-------------------------------------------------------<BR>
>>the temperature extracted after the simulations<BR>
>>-------------------------------------------------------<BR>
>>s0 legend "Temperature"<BR>
>> 0.000000 376.058044<BR>
>> 1.000000 864.033020<BR>
>> 2.000000 873.607605<BR>
>> 3.000000 851.308838<BR>
>> 4.000000 847.223877<BR>
>> 5.000000 860.511841<BR>
>> 6.000000 813.547241<BR>
>> 7.000000 845.261658<BR>
>> 8.000000 872.090027<BR>
>> 9.000000 852.079468<BR>
>> 10.000000 849.152466<BR>
>> 11.000001 850.055237<BR>
>> 12.000001 834.468323<BR>
>> 13.000001 861.107300<BR>
>> 14.000001 828.380493<BR>
>> 15.000001 850.166809<BR>
>> 16.000000 850.382019<BR>
>> 17.000000 847.214478<BR>
>> 18.000000 851.201538<BR>
>> 19.000000 857.533691<BR>
>> 20.000000 849.760071<BR>
>> 21.000002 864.907715<BR>
>> 22.000002 837.307495<BR>
>> 23.000002 827.407593<BR>
>> 24.000002 841.464111<BR>
>> 25.000002 863.330688<BR>
>> 26.000002 841.096069<BR>
>> 27.000002 856.469910<BR>
>> 28.000002 854.449768<BR>
>> 29.000002 845.534973<BR>
>> 30.000002 853.421448<BR>
>> 31.000002 825.198059<BR>
>> 32.000000 857.317566<BR>
>> 33.000000 823.510925<BR>
>> 34.000000 858.875122<BR>
>> 35.000000 880.710266<BR>
>> 36.000000 853.692749<BR>
>> 37.000000 847.079468<BR>
>> 38.000000 851.004822<BR>
>> 39.000000 858.750000<BR>
>> 40.000000 872.787048<BR>
>> 41.000004 843.033813<BR>
>> 42.000004 874.984009<BR>
>> 43.000004 845.272583<BR>
>> 44.000004 822.993713<BR>
>> 45.000004 863.116455<BR>
>> 46.000004 865.640198<BR>
>> 47.000004 873.489563<BR>
>> 48.000004 849.170776<BR>
>> 49.000004 861.631958<BR>
>> 50.000004 860.999939<BR>
>> 51.000004 834.341003<BR>
>> 52.000004 864.601196<BR>
>> 53.000004 838.268372<BR>
>> 54.000004 842.860046<BR>
>> 55.000004 837.590332<BR>
>> 56.000004 855.985046<BR>
>> 57.000004 836.168030<BR>
>> 58.000004 862.147644<BR>
>> 59.000004 869.183044<BR>
>> 60.000004 873.057556<BR>
>> 61.000004 871.051636<BR>
>> 62.000004 857.647217<BR>
>> 63.000004 857.834106<BR>
>> 64.000000 871.380981<BR>
>> 65.000000 850.045654<BR>
>> 66.000000 880.142456<BR>
>> 67.000000 844.183350<BR>
>> 68.000000 850.980042<BR>
>> 69.000000 854.431091<BR>
>> 70.000000 847.898743<BR>
>> 71.000000 859.750488<BR>
>> 72.000000 852.219910<BR>
>> 73.000000 854.833984<BR>
>> 74.000000 851.676514<BR>
>> 75.000000 866.519287<BR>
>> 76.000000 861.120605<BR>
>> 77.000000 857.873230<BR>
>> 78.000000 845.287720<BR>
>> 79.000000 874.603333<BR>
>> 80.000000 854.244751<BR>
>> 81.000008 864.049561<BR>
>> 82.000008 892.515991<BR>
>> 83.000008 855.164734<BR>
>> 84.000008 867.054077<BR>
>> 85.000008 862.560059<BR>
>> 86.000008 829.368469<BR>
>> 87.000008 864.729553<BR>
>> 88.000008 882.954102<BR>
>> 89.000008 865.048401<BR>
>> 90.000008 864.581848<BR>
>> 91.000008 870.596619<BR>
>> 92.000008 856.474976<BR>
>> 93.000008 861.473450<BR>
>> 94.000008 838.902344<BR>
>> 95.000008 896.907715<BR>
>> 96.000008 865.042480<BR>
>> 97.000008 877.761292<BR>
>> 98.000008 877.356750<BR>
>> 99.000008 855.421753<BR>
>> 100.000008 863.720398<BR>
>> ------------------------------------------------------<BR>
>><BR>
>>Could anyone tell me what changes I should make in the parameter file?<BR>
>><BR>
>><BR>
>><BR>
>>Many thanks,<BR>
>>Jes.<BR>
>><BR>
>><BR>
>><BR>
>><BR>
>><BR>
>><BR>
>> <BR>
><BR>
>-----------------------------------------------------<BR>
>XAvier Periole - PhD<BR>
><BR>
>- Molecular Dynamics Group -<BR>
>NMR and Computation<BR>
>University of Groningen<BR>
>The Netherlands<BR>
>-----------------------------------------------------<BR>
</P>
<br><br>
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