<P>
<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>
; 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>
-------------------------------------------------------<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>
</P>
<br><br>
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