[gmx-users] SIMULATED ANNEALING

Thu Feb 12 13:35:37 CET 2009

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.
Kindly comment. 
sharada
Re: [gmx-users] how to write a annealing .mdp
Qiao Baofu
Wed, 13 Sep 2006 05:04:30 -0700
Hi,
  set T_couple=no and refer to the following script
; SIMULATED ANNEALING  
; Type of annealing for each temperature group (no/single/periodic)
annealing                = single
; Number of time points to use for specifying annealing in each group 
annealing_npoints        = 6
; List of times at the annealing points for each group
annealing_time           = 0 10 20 30 40 50
; Temp. at each annealing point, for each group.
annealing_temp           = 425 375 325 275 245 203 
06-9-13zzhwise1 <[EMAIL PROTECTED]> 
hello everyone
      i want to anneal my system,but i don't konw how to wrote a right annealing-mdp!
could anyone give me a moldel?
  tanks in advaced!
-- Original Message --
From: Nuno Azoia <nazoia at det.uminho.pt>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Thu, 12 Feb 2009 12:22:43 +0000
Subject: Re: [gmx-users] (no subject)
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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