[gmx-users] (no subject)
sharada
sharada at ccmb.res.in
Thu Feb 12 13:02:33 CET 2009
Dear gromacs-users,
I am heating a peptidein methanol from 0K - 300K. The simulated annealing protocol is given in the md.mdp file shown below:
------------------------------------------------
title = cpeptide MD
cpp = /lib/cpp
constraints = all-bonds
integrator = md
tinit = 0.0
dt = 0.002 ; ps !leapfrog algorithm 2fs timestep
nsteps = 500000 ; total 2 ns.
nstcomm = 1
nstxout = 10000
nstvout = 5000
nstfout = 0
nstlist = 5
ns_type = grid
pbc = xyz
coulombtype = PME
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.5
epsilon_r = 32.0
; Berendsen temperature coupling is on in two groups
Tcoupl = no
tau_t = 0 0
tc-grps = protein other
ref_t = 50 50
solvent_optimization = sol
; Energy monitoring
energygrps = Protein other
; Pressure coupling is on
Pcoupl = Berendsen
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = single single
; Number of time points to use for specifying annealing in each group
annealing_npoints = 9 9
; List of times at the annealing points for each group
annealing_time = 0 10 20 30 40 50 60 70 80 0 10 20 30 40 50 60 70 80
; Temp. at each annealing point, for each group.
annealing_temp = 50 80 110 140 170 200 230 260 300 50 80 110 140 170 200 230 260 300
; Generate velocites is on at 50 K.
gen_vel = no
gen_temp = 50.0
gen_seed = 173529
----------------------------------------------
This is the output of the run ...
Current ref_t for group Protein: 50.0
Current ref_t for group Other: 50.0
Energies (kJ/mol)
Angle G96Angle Proper Dih. Improper Dih. LJ-14
1.51438e+02 1.57246e+02 9.67560e+01 3.39340e+01 -1.86728e+00
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
1.11363e+02 -5.80246e+04 -8.11824e+02 -4.91976e+02 -2.26900e+02
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-5.90065e+04 5.82281e+03 -5.31836e+04 4.99176e+01 -1.00344e+03
Step Time Lambda
100 0.20000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.002846 58 59 0.000439
After LINCS 0.000010 105 107 0.000001
Current ref_t for group Protein: 50.6
Current ref_t for group Other: 50.6
Energies (kJ/mol)
Angle G96Angle Proper Dih. Improper Dih. LJ-14
1.38141e+02 1.48331e+02 1.05076e+02 3.22396e+01 -3.30152e+00
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
1.10745e+02 -5.83654e+04 -8.23368e+02 -4.82819e+02 -2.28454e+02
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-5.93689e+04 5.94610e+03 -5.34228e+04 5.09746e+01 -7.78032e+02
Step Time Lambda
200 0.40000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.003484 5534 5535 0.000426
After LINCS 0.000007 66 67 0.000001
Current ref_t for group Protein: 51.2
Current ref_t for group Other: 51.2
Energies (kJ/mol)
Angle G96Angle Proper Dih. Improper Dih. LJ-14
1.43780e+02 1.37908e+02 1.03575e+02 3.10259e+01 2.92268e+00
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
1.11216e+02 -5.86508e+04 -8.31542e+02 -4.89405e+02 -2.23838e+02
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-5.96652e+04 6.12069e+03 -5.35445e+04 5.24713e+01 -4.88928e+02
Step Time Lambda
300 0.60000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.002752 5792 5793 0.000424
After LINCS 0.000008 105 107 0.000001
Current ref_t for group Protein: 51.8
Current ref_t for group Other: 51.8
Energies (kJ/mol)
Angle G96Angle Proper Dih. Improper Dih. LJ-14
1.48813e+02 1.42970e+02 1.03284e+02 3.23617e+01 -4.37215e+00
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
1.11596e+02 -5.88305e+04 -8.37264e+02 -4.92025e+02 -2.29802e+02
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-5.98550e+04 6.24111e+03 -5.36139e+04 5.35036e+01 -2.18755e+02
Step Time Lambda
400 0.80000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.003186 5135 5136 0.000428
After LINCS 0.000007 45 46 0.000001
Current ref_t for group Protein: 52.4
Current ref_t for group Other: 52.4
Energies (kJ/mol)
Angle G96Angle Proper Dih. Improper Dih. LJ-14
1.48258e+02 1.34671e+02 9.78242e+01 3.23113e+01 2.68271e+00
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
1.11526e+02 -5.88899e+04 -8.39509e+02 -5.12034e+02 -2.29234e+02
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-5.99434e+04 6.28344e+03 -5.36599e+04 5.38665e+01 -8.48820e+01
Step Time Lambda
500 1.00000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.003304 7457 7458 0.000434
After LINCS 0.000007 189 190 0.000001
---
---
---
---
Current ref_t for group Protein: 300.0
Current ref_t for group Other: 300.0
Energies (kJ/mol)
Angle G96Angle Proper Dih. Improper Dih. LJ-14
1.32540e+02 1.42359e+02 8.84796e+01 3.64486e+01 2.81073e+00
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
1.11433e+02 -6.05890e+04 -8.96227e+02 -4.56756e+02 -2.26580e+02
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-6.16545e+04 7.10020e+03 -5.45543e+04 6.08684e+01 -2.20348e+01
---------------------------------------------------------------------------
The problem is the temperature of the system is remaining at 60K even when ref_t goes to 300K. I have shown some portion of the output for your information. Why is this happening ? Kindly help.
thankyou
sharada
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