[gmx-users] simulated annealing
tarak karmakar
tarak20489 at gmail.com
Tue Nov 6 05:14:30 CET 2012
Dear All,
In my test simulation annealing I'm trying to heat my system from 0 K
to 300 k after 10 ps of run. But at the end I see the temperature
didn't reach to 300 K , it's near around 22 K.
So can anyone please correct me in my .mdp file ?
constraints = none
integrator = md-vv
dt = 0.0005 ; 1fs
nsteps = 20000 ; 30ps
nstcomm = 1
nstxout = 1000 ; frequency to write
coordinates to output trajectory
nstvout = 0 ; frequency to write
velocities to output trajectory; the last velocities are always
written
nstfout = 0 ; frequency to write forces to
output trajectory
nstlog = 1000 ; frequency to write
energies to log file
nstenergy = 1000 ; frequency to write energies to edr file
nstcalcenergy = 1000
vdwtype = cut-off
coulombtype = PME
pbc = xyz
table-extension = 20.0
nstlist = 100
ns_type = grid
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
comm-grps = system
optimize_fft = yes
;heating
annealing = single
annealing_npoints = 2
annealing_time = 0 10
annealing_temp = 0 300
ld_seed = 8072012
;nsttcouple = 0.001
;temperature coupling is on
Tcoupl = Nose-Hoover
tau_t = 1.0
tc_grps = system
ref_t = 0
;Pressure coupling is off
Pcoupl = no
; Generate velocites is on
gen_vel = yes
gen_temp = 0
gen_seed = 8042012
THE .log FILE
Constraining the starting coordinates (step 0)
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 0 K
Started mdrun on node 0 Tue Nov 6 21:21:05 2012
Step Time Lambda
0 0.00000 0.00000
Grid: 14 x 14 x 14 cells
Current ref_t for group System: 0.0
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
6.98365e+02 2.31495e+03 4.34144e+03 9.32563e+01 3.06280e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
4.90527e+04 3.16274e+05 -1.60409e+06 -1.10076e+05 -1.33833e+06
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
0.00000e+00 -1.33833e+06 -1.33833e+06 0.00000e+00 1.63793e+02
Step Time Lambda
1000 0.50000 0.00000
Current ref_t for group System: 15.0
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
5.91509e+02 2.27120e+03 4.37612e+03 1.01524e+02 3.13151e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
4.91902e+04 2.58594e+05 -1.55303e+06 -1.10344e+05 -1.34512e+06
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
6.82988e+03 -1.33829e+06 -1.33829e+06 1.08252e+01 -4.10650e+03
Step Time Lambda
2000 1.00000 0.00000
Current ref_t for group System: 30.0
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
5.90602e+02 2.30240e+03 4.39329e+03 1.10298e+02 3.15642e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
4.91731e+04 2.60786e+05 -1.55644e+06 -1.10395e+05 -1.34632e+06
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
8.05310e+03 -1.33827e+06 -1.33827e+06 1.27640e+01 -3.72695e+03
..............
..............
Current ref_t for group System: 255.0
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
6.07478e+02 2.34899e+03 4.43725e+03 1.08744e+02 3.17997e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
4.91213e+04 2.69271e+05 -1.57036e+06 -1.10532e+05 -1.35182e+06
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.39095e+04 -1.33791e+06 -1.33791e+06 2.20464e+01 -3.08283e+03
Step Time Lambda
18000 9.00000 0.00000
Current ref_t for group System: 270.0
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
6.22035e+02 2.35774e+03 4.41413e+03 1.07439e+02 3.16535e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
4.91418e+04 2.69872e+05 -1.57111e+06 -1.10528e+05 -1.35195e+06
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.40644e+04 -1.33789e+06 -1.33789e+06 2.22919e+01 -3.09464e+03
Step Time Lambda
19000 9.50000 0.00000
Current ref_t for group System: 285.0
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
6.31355e+02 2.37456e+03 4.40719e+03 1.06998e+02 3.16961e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
4.90783e+04 2.69394e+05 -1.57063e+06 -1.10548e+05 -1.35202e+06
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.41424e+04 -1.33788e+06 -1.33788e+06 2.24154e+01 -3.29328e+03
Step Time Lambda
20000 10.00000 0.00000
Writing checkpoint, step 20000 at Tue Nov 6 21:39:16 2012
Current ref_t for group System: 300.0
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
6.25626e+02 2.36220e+03 4.42870e+03 1.05787e+02 3.16930e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
4.91428e+04 2.69664e+05 -1.57107e+06 -1.10530e+05 -1.35210e+06
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.42464e+04 -1.33786e+06 -1.33786e+06 2.25803e+01 -3.15481e+03
Thanks for ur help.
--
Tarak
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