[gmx-users] SIMULATED ANNEALING

Fri Feb 13 07:18:38 CET 2009

Thankyou for the reply Mark.  In fact I started another simulated annealing job for my peptide with Tcoupl = Berendsen using the same annealing protocol. I didnot get any warnings. However the temperature increases from 0 to 53K and fluctuates around that through out till the end of the simulation. I am attaching the Averages and RMS values for the various components that its calculating. As you can see the average Temp is around 56 -58. Why is this not increasing beyound that?  I would also like to know if  the RMS fluctuations are in the required range , further if the system is behaving as an NVE ensemble which I don't intend to do right now what parameters I should correct in order to achieve an NPT ensemble.  Density of methanol is maintained, however the box sizes are reduced slightly from (editconf -f 2MLT_pdb2gmx.gro -o 2MLT_box.gro -bt octahedron -box 6.9 6.9 6.9) to the ones as shown below.  Kindly guide me through.
Regards
sharada
#############  ==>
 <====  A V E R A G E S  ====>
 <==  ###############  ======>
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
    1.25569e+02    1.45264e+02    8.14163e+01    3.35938e+01   -4.14588e+00
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coul. recip.
    1.11566e+02   -6.13052e+04   -9.02963e+02   -4.90858e+02   -2.29446e+02
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -6.24352e+04    6.55473e+03   -5.58804e+04    5.61922e+01   -6.44581e-01
          Box-X          Box-Y          Box-Z         Volume   Density (SI)
    6.59352e+00    6.21552e+00    5.38142e+00    2.20549e+02    9.71762e+02
             pV
   -1.00030e+01
   Total Virial (kJ/mol)
    2.20235e+03    1.73889e+01    3.30993e+01
    1.73889e+01    2.19217e+03    3.10533e+01
    3.30993e+01    3.10533e+01    2.17521e+03
   Pressure (bar)
   -3.38055e+00   -2.23803e+00   -5.33957e+00
   -2.23802e+00   -6.64252e-01   -4.91175e+00
   -5.33957e+00   -4.91175e+00    2.11106e+00
   Total Dipole (Debye)
    1.27755e+02    3.52104e+02    3.75237e+02
  Epot (kJ/mol)        Coul-SR          LJ-SR          LJ-LR        Coul-14          LJ-14   
Protein-Protein   -3.40720e+01   -6.16549e+02   -2.13677e+00    1.11566e+02   -4.14588e+00
  Protein-Other   -1.39464e+01   -1.18676e+03   -3.93175e+01    0.00000e+00    0.00000e+00
    Other-Other   -4.42840e+02   -5.95019e+04   -8.61509e+02    0.00000e+00    0.00000e+00
      T-Protein        T-Other
    5.81959e+01    5.61543e+01
 <======  ###############################  ==>
 <====  R M S - F L U C T U A T I O N S  ====>
 <==  ###############################  ======>
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
    3.63607e+00    8.07621e+00    5.91745e+00    3.68058e+00    6.03747e+00
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coul. recip.
    3.94884e-01    5.68584e+02    7.51264e+00    2.60823e+01    5.45860e+00
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
    6.06744e+02    3.31755e+02    9.21157e+02    2.84406e+00    2.89776e+01
          Box-X          Box-Y          Box-Z         Volume   Density (SI)
    2.05639e-02    1.97767e-02    1.78224e-02    2.14976e+00    9.09307e+00
             pV
    4.03650e+02
   Total Virial (kJ/mol)
    3.48732e+02    2.38190e+02    2.34143e+02
    2.38190e+02    3.58063e+02    2.29927e+02
    2.34143e+02    2.29927e+02    3.69445e+02
   Pressure (bar)
    4.96979e+01    3.61135e+01    3.53962e+01
    3.61135e+01    5.04350e+01    3.47331e+01
    3.53962e+01    3.47331e+01    5.09166e+01
   Total Dipole (Debye)
    8.26716e+01    8.83756e+01    9.41694e+01
  Epot (kJ/mol)        Coul-SR          LJ-SR          LJ-LR        Coul-14          LJ-14   
Protein-Protein    8.03847e-01    5.52640e+00    5.38082e-02    3.94884e-01    6.03747e+00
  Protein-Other    2.33155e+00    1.42410e+01    4.03903e-01    0.00000e+00    0.00000e+00
    Other-Other    2.54858e+01    5.55314e+02    7.27596e+00    0.00000e+00    0.00000e+00
      T-Protein        T-Other
    4.00791e+00    2.87110e+00
-- Original Message --
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Fri, 13 Feb 2009 00:13:23 +1100
Subject: Re: [gmx-users] SIMULATED ANNEALING
sharada wrote:
> Dear Nuno Azoia,
> 
> I followed one of the replies given at gmx-users list which I quote 
> here...I donot know whether this is right ? In that case the temperature 
> has truly changed from 0 to 60 how is it possible if Tcoupl = no...?I 
> am in doubt.
You're actually running in an NVE ensemble, which hasn't yet reached its 
natural equilibrium temperature.
Perhaps there should be a grompp warning for when simulated annealing is 
attempted without temperature coupling...
Mark
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