[gmx-developers] md-vv and v-rescale thermostat?
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Sep 3 15:43:05 CEST 2012
Hi,
I tried the md-vv integrator in release-4-5-patches (2859895) in concert
with the v-rescale (Bussi) thermostat and found some weird heating
behaviour on a 900-TIP3P system that was fine with the md integrator.
(.mdp file at end of email) Michael (or anybody else) is/was this
thermostat known to work with md-vv?
With md-vv:
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
1.56788e+04 -2.52945e+02 -3.58017e+04 -3.73679e+03 -2.41127e+04
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
9.86312e+03 -1.42495e+04 -1.42495e+04 4.39597e+02 -1.54019e+02
Pressure (bar)
-5.69569e+04
Step Time Lambda
500 1.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
8.23626e+03 -2.52945e+02 -1.74349e+04 -3.27515e+03 -1.27267e+04
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
4.19512e+04 2.92245e+04 2.45247e+04 1.86976e+03 -1.54019e+02
Pressure (bar)
2.97051e+04
<snip>
Step Time Lambda
500000 1000.00000 0.00000
Writing checkpoint, step 500000 at Mon Sep 3 23:15:57 2012
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
1.01917e+04 -2.52945e+02 -1.51940e+04 -3.02693e+03 -8.28214e+03
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
5.17784e+04 4.34963e+04 4.79009e+04 2.30775e+03 -1.54019e+02
Pressure (bar)
3.82536e+04
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 500001 steps using 50001 frames
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
9.71441e+03 -2.52945e+02 -1.51389e+04 -3.03171e+03 -8.70917e+03
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
5.25444e+04 4.38352e+04 4.10799e+04 2.34189e+03 -1.54019e+02
Pressure (bar)
3.73202e+04
Obviously this is heating massively at the start and the thermostat is
totally failing to deal with it. With integrator md:
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
1.56788e+04 -2.52945e+02 -3.58017e+04 -3.73679e+03 -2.41127e+04
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
1.30540e+04 -1.10587e+04 -1.10587e+04 5.81814e+02 -1.54019e+02
Pressure (bar)
-1.29542e+04
Step Time Lambda
500 1.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
4.57027e+03 -2.52945e+02 -3.01897e+04 -4.38326e+03 -3.02556e+04
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
1.07502e+04 -1.95054e+04 -1.39359e+04 4.79135e+02 -1.54019e+02
Pressure (bar)
3.29939e+03
<snip>
Step Time Lambda
500000 1000.00000 0.00000
Writing checkpoint, step 500000 at Wed Aug 29 01:54:51 2012
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
5.72530e+03 -2.52945e+02 -3.72877e+04 -4.50918e+03 -3.63246e+04
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
6.59347e+03 -2.97311e+04 -1.25805e+04 2.93870e+02 -1.54019e+02
Pressure (bar)
-1.82664e+02
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 500001 steps using 50001 frames
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
5.74509e+03 -2.52945e+02 -3.72807e+04 -4.52328e+03 -3.63118e+04
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
6.58722e+03 -2.97246e+04 -1.32539e+04 2.93591e+02 -1.54019e+02
Pressure (bar)
-4.77602e+01
This looks fine.
Mark
; VARIOUS PREPROCESSING OPTIONS
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