On 2/19/18 2:38 PM, Ahmed Mashaly wrote:
So I redo the NVT with ref-t and gen-temp set to zero or I neglect this issue?
Kind Regards,Ahmed
If your goal is to heat from 0->300 K, then I'd suggest you do that
rather than starting at 300 K, attempting to beat the system into
submission and trying to heat. Or you could bypass heating altogether
and just do a typical 300 K equilibration directly. I guess that
depends on what your system needs, but I've rarely found value in taking
the time to heat the system up.
-Justin
From: Justin Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
Sent: Monday, February 19, 2018 8:33 PM
Subject: Re: [gmx-users] simulated annealing
On 2/19/18 2:31 PM, Ahmed Mashaly wrote:
Thanks, Justin.
I had set it to 300K before (as the original mdp was), but now I found others
with 0
Now when if we look at the log file, you can see ref temp for both groups
starts from 0 and increasing, but the temperature in the details goes from 300
to 5 to 2, then it starts increasing again:
----------------------------------------------------------------------
Started mdrun on rank 0 Thu Feb 15 06:00:49 2018
Step Time
0 0.00000
Current ref_t for group Protein: 0.0
Current ref_t for group non-Protein: 0.0
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.51283e+03 1.20582e+04 6.93519e+04 6.27988e+02 1.88294e+04
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.26883e+05 7.62987e+05 -3.36842e+04 -5.35584e+06 1.97969e+04
Potential Kinetic En. Total Energy Conserved En. Temperature
-4.27548e+06 7.07199e+05 -3.56828e+06 -3.56828e+06 3.00605e+02
Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.86887e+02 1.45163e+03 4.71563e-06
DD step 19 load imb.: force 93.3% pme mesh/force 1.284
step 40 Turning on dynamic load balancing, because the performance loss due to
load imbalance is 3.6 %.
DD load balancing is limited by minimum cell size in dimension Y
DD step 499 vol min/aver 0.501! load imb.: force 6.8% pme mesh/force 0.849
Step Time
500 1.00000
Current ref_t for group Protein: 0.6
Current ref_t for group non-Protein: 0.6
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.46055e+03 1.23246e+04 6.95866e+04 6.62756e+02 1.87622e+04
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.26321e+05 7.48416e+05 -3.36842e+04 -5.50170e+06 1.60271e+04
Potential Kinetic En. Total Energy Conserved En. Temperature
-4.43983e+06 1.20712e+04 -4.42776e+06 -3.56007e+06 5.13104e+00
Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.86887e+02 -1.52962e+03 2.60669e-06
DD load balancing is limited by minimum cell size in dimension Y
DD step 999 vol min/aver 0.536! load imb.: force 4.4% pme mesh/force 0.719
Step Time
1000 2.00000
Current ref_t for group Protein: 1.2
Current ref_t for group non-Protein: 1.2
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.36670e+03 1.22399e+04 6.95391e+04 6.50404e+02 1.87726e+04
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.26254e+05 7.67224e+05 -3.36842e+04 -5.55850e+06 1.52291e+04
Potential Kinetic En. Total Energy Conserved En. Temperature
-4.47891e+06 5.32623e+03 -4.47359e+06 -3.56020e+06 2.26399e+00
Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.86887e+02 -1.51090e+03 2.52820e-06
DD load balancing is limited by minimum cell size in dimension Y
DD step 1499 vol min/aver 0.568! load imb.: force 3.1% pme mesh/force 0.727
Step Time
1500 3.00000
Current ref_t for group Protein: 1.8
Current ref_t for group non-Protein: 1.8
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.30312e+03 1.22047e+04 6.95879e+04 6.55239e+02 1.88651e+04
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.26345e+05 7.77640e+05 -3.36842e+04 -5.58600e+06 1.46894e+04
Potential Kinetic En. Total Energy Conserved En. Temperature
-4.49639e+06 5.57315e+03 -4.49082e+06 -3.56022e+06 2.36895e+00
Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.86887e+02 -1.43160e+03 2.50109e-06
---------------------------------------------------------------------
And when I used gmx energy to generate temp curve, I got this at the beginning:
0.000000 300.605164 300.543854 300.611908
1.000000 5.131036 3.108571 5.354491
2.000000 2.263988 1.550216 2.342851
3.000000 2.368947 1.869242 2.424157
4.000000 2.709096 2.333785 2.750562
5.000000 3.236674 3.030164 3.259491
6.000000 3.733118 3.523592 3.756267
7.000000 4.282474 3.992255 4.314539
8.000000 4.829560 4.523222 4.863406
9.000000 5.418922 5.164090 5.447078
Also I noticed a shrink in the water box after NVT, and it expands to the usual
at the start of NPT, is the shrink realted to this?
Possibly. If you tell the system it's at 300 K, but then force the
thermostat to try to damp the velocities down to zero, you're going to
get weird physical behavior.
-Justin
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