[gmx-users] (no subject)

Nuno Azoia nazoia at det.uminho.pt
Thu Feb 12 13:22:43 CET 2009


I don't have so much experience, but I found something strange in our
mdp file.

>; Berendsen temperature coupling is on in two groups
> Tcoupl              =  no
> tau_t               =  0           0

In my opinion, I think that if you have Tcoupl = no you can't expect the
temperature of your system to chage.

Nuno Azoia

On Thu, 2009-02-12 at 17:32 +0530, sharada wrote:
> 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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