[gmx-users] simulated annealing
Christopher Neale
chris.neale at mail.utoronto.ca
Tue Nov 6 07:07:33 CET 2012
your tau_t is 1 ps and you want to increase the temperature by 300 K in 10 ps. I doubt that this is possible.
Try heating over a longer period of time. The longer the period, the closer you will get to your target temperature.
Why do you need to do the heating over 10 ps? Also, when using any deterministic integrator, I think that you are
asking for problems anyway based on a rapid scaling of forces into velocities. Try doing this over 1 ns instead. The
alternative, reducing tau_t, is not a good idea.
Chris.
-- original message --
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.
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