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.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@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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