[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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