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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