[gmx-users] High Temperatures in NVT
Mark Abraham
mark.j.abraham at gmail.com
Fri Mar 15 11:51:07 CET 2013
A single frame proves very little. You should be looking at the trends in
(say) average values in observables relevant to what you're going to want
the simulation to sample. It's a bit of a dark art, however.
Mark
On Fri, Mar 15, 2013 at 11:02 AM, Abhishek Acharya <aacharya at iitk.ac.in>wrote:
> Thanks for replying Mark
> So in that case, i presume a proper npt run should indicate all is
> well with the system. Since there was nothing wrong in the output .gro
> file of nvt and also the npt run was alright , should i go ahead with
> the production run ?
> Abhishek
>
>
> What happens when you take a children's swing in the playground, place it
> > in some crazy position and push it off in some random direction? The
> swing
> > will swing, but it won't look "proper" for a while. Apparently your
> > initial
> > conditions are a bit crazy, e.g. some void next to your solute where a
> > solvent molecule couldn't quite fit... :-)
> >
> > Mark
> >
> > On Fri, Mar 15, 2013 at 7:48 AM, Abhishek Acharya
> > <aacharya at iitk.ac.in>wrote:
> >
> >> Hello Gromacs Users.
> >> I ran an NVT simulation and i noticed that after the initial step at
> >> 300K
> >> the temperature shoots up to order of 10^3 and then suddenly comes down
> >> around 300K. Is there something wrong with the system or is this normal
> >> to
> >> see such fluctuations ? There was no warning and the equilibration ran
> >> properly.Thereafter i also ran an NPT equilibaration, in which the
> >> temperature was maintained at 300K throughout. I can't understand why do
> >> i
> >> see such high temperature and why the system didn't blow up at such a
> >> temp.
> >> Any thoughts ??
> >>
> >> I used V-rescale and set temperature to 300K.
> >>
> >> Partial Output of the run is given below:
> >>
> >> Constraining the coordinates at t0-dt (step 0)
> >> RMS relative constraint deviation after constraining: 5.41e-05
> >> Initial temperature: 300.665 K
> >>
> >> Started mdrun on node 0 Sun Mar 10 12:29:30 2013
> >>
> >> Step Time Lambda
> >> 0 0.00000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 5.85999e+03 1.73773e+04 2.56754e+02 2.87887e+02
> >> 6.36875e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.05209e+04 1.35894e+05 -9.32374e+03 -1.29691e+06
> >> 6.02106e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 3.07790e+00 -1.06364e+06 1.72203e+05 -8.91438e+05
> >> -8.91438e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 3.00732e+02 -2.24892e+02 -6.01369e+03 4.95520e-05
> >>
> >> Step Time Lambda
> >> 10 0.02000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.07859e+04 1.80238e+04 2.62454e+02 5.40121e+02
> >> 7.32982e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.09087e+04 1.62006e+05 -9.32374e+03 -1.25168e+06
> >> 6.58684e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 1.33127e+02 -9.84429e+05 1.42626e+06 4.41834e+05
> >> 4.42290e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 2.49080e+03 -2.24892e+02 2.15463e+04 2.06703e-05
> >>
> >> Step Time Lambda
> >> 20 0.04000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.03629e+04 1.81746e+04 2.63472e+02 5.99622e+02
> >> 7.55735e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.14113e+04 1.64419e+05 -9.32374e+03 -1.25426e+06
> >> 6.65214e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 3.29278e+02 -9.83818e+05 8.19856e+05 -1.63962e+05
> >> -1.63507e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.43178e+03 -2.24892e+02 1.20551e+04 1.67346e-05
> >>
> >> Step Time Lambda
> >> 30 0.06000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 9.21495e+03 1.81436e+04 2.67028e+02 6.35385e+02
> >> 7.56268e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.15424e+04 1.44261e+05 -9.32374e+03 -1.23407e+06
> >> 6.59806e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 5.35759e+02 -9.84635e+05 7.90514e+05 -1.94120e+05
> >> -1.93665e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.38054e+03 -2.24892e+02 1.01709e+04 1.65873e-05
> >>
> >> Step Time Lambda
> >> 40 0.08000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 9.57235e+03 1.83147e+04 2.81327e+02 5.54864e+02
> >> 7.33138e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.13699e+04 1.36309e+05 -9.32374e+03 -1.22425e+06
> >> 6.51767e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 7.27259e+02 -9.82598e+05 7.98608e+05 -1.83990e+05
> >> -1.83535e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.39468e+03 -2.24892e+02 9.60979e+03 1.76827e-05
> >>
> >> Step Time Lambda
> >> 50 0.10000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.02210e+04 1.82222e+04 2.73159e+02 5.94300e+02
> >> 7.23755e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.09596e+04 1.33188e+05 -9.32374e+03 -1.21864e+06
> >> 6.24436e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 9.17212e+02 -9.80111e+05 7.80934e+05 -1.99177e+05
> >> -1.98722e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.36381e+03 -2.24892e+02 8.90814e+03 2.09207e-05
> >>
> >> Step Time Lambda
> >> 60 0.12000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.05104e+04 1.80778e+04 2.80711e+02 5.10204e+02
> >> 7.33378e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.12876e+04 1.30953e+05 -9.32374e+03 -1.21819e+06
> >> 6.13229e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 1.11549e+03 -9.81308e+05 7.67206e+05 -2.14103e+05
> >> -2.13648e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.33983e+03 -2.24892e+02 8.47552e+03 1.93736e-05
> >>
> >> Step Time Lambda
> >> 70 0.14000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 9.75644e+03 1.81003e+04 2.68350e+02 5.67122e+02
> >> 7.32276e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.15854e+04 1.31124e+05 -9.32374e+03 -1.21940e+06
> >> 5.91323e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 1.31786e+03 -9.82770e+05 7.76555e+05 -2.06215e+05
> >> -2.05760e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.35616e+03 -2.24892e+02 8.44854e+03 1.98273e-05
> >>
> >> Step Time Lambda
> >> 80 0.16000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 9.99579e+03 1.80240e+04 2.70956e+02 5.87449e+02
> >> 7.30852e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.14808e+04 1.32143e+05 -9.32374e+03 -1.22208e+06
> >> 5.86487e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 1.51222e+03 -9.84218e+05 7.86806e+05 -1.97412e+05
> >> -1.96957e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.37407e+03 -2.24892e+02 8.68540e+03 1.89887e-05
> >>
> >> Step Time Lambda
> >> 90 0.18000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.00927e+04 1.80655e+04 2.74654e+02 5.33909e+02
> >> 7.19358e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.12502e+04 1.33801e+05 -9.32374e+03 -1.22545e+06
> >> 5.64114e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 1.69598e+03 -9.86228e+05 8.00800e+05 -1.85428e+05
> >> -1.84972e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.39850e+03 -2.24892e+02 8.81495e+03 2.07088e-05
> >>
> >> DD step 99 load imb.: force 7.7%
> >>
> >> At step 100 the performance loss due to force load imbalance is 6.3 %
> >>
> >> NOTE: Turning on dynamic load balancing
> >>
> >> Step Time Lambda
> >> 100 0.20000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.01106e+04 1.80406e+04 2.62235e+02 6.01307e+02
> >> 7.18058e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.10367e+04 1.36420e+05 -9.32374e+03 -1.22936e+06
> >> 5.67431e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 1.85081e+03 -9.87506e+05 9.72319e+04 -8.90274e+05
> >> -8.89819e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.69804e+02 -2.24892e+02 -2.38234e+03 2.10635e-05
> >>
> >> Step Time Lambda
> >> 110 0.22000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.21659e+04 1.83414e+04 2.68670e+02 6.14380e+02
> >> 7.60930e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.14218e+04 1.46855e+05 -9.32374e+03 -1.21576e+06
> >> 5.98482e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 2.06107e+03 -9.59761e+05 8.45193e+05 -1.14568e+05
> >> -1.78964e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.47603e+03 -2.24892e+02 1.12440e+04 2.27605e-05
> >>
> >> Step Time Lambda
> >> 120 0.24000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.20402e+04 1.82851e+04 2.69269e+02 7.15817e+02
> >> 7.52215e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.13053e+04 1.50789e+05 -9.32374e+03 -1.22104e+06
> >> 5.86532e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 2.27267e+03 -9.61300e+05 1.14729e+06 1.85992e+05
> >> 1.21596e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 2.00361e+03 -2.24892e+02 1.62006e+04 2.27024e-05
> >>
> >> Step Time Lambda
> >> 130 0.26000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.17779e+04 1.83401e+04 2.70022e+02 6.30376e+02
> >> 7.48596e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.13089e+04 1.46156e+05 -9.32374e+03 -1.21415e+06
> >> 6.03188e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 2.45197e+03 -9.59020e+05 1.15119e+06 1.92170e+05
> >> 1.27773e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 2.01042e+03 -2.24892e+02 1.58943e+04 2.33979e-05
> >>
> >> Step Time Lambda
> >> 140 0.28000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.19184e+04 1.82552e+04 2.66851e+02 7.42218e+02
> >> 7.42258e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.11204e+04 1.41882e+05 -9.32374e+03 -1.20810e+06
> >> 5.86417e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 2.56536e+03 -9.57388e+05 1.13362e+06 1.76232e+05
> >> 1.11835e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.97973e+03 -2.24892e+02 1.52716e+04 2.42128e-05
> >>
> >> Step Time Lambda
> >> 150 0.30000 0.00000
> >>
> >> Energies (kJ/mol)
> >> Angle Proper Dih. Ryckaert-Bell. Improper Dih.
> >> LJ-14
> >> 1.23089e+04 1.82970e+04 2.57919e+02 6.45844e+02
> >> 7.39740e+03
> >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> >> recip.
> >> 7.12356e+04 1.38777e+05 -9.32374e+03 -1.20341e+06
> >> 5.95655e+03
> >> Position Rest. Potential Kinetic En. Total Energy Conserved
> >> En.
> >> 2.61103e+03 -9.55251e+05 1.12033e+06 1.65074e+05
> >> 1.00678e+05
> >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
> >> 1.95652e+03 -2.24892e+02 1.49190e+04 2.42873e-05
> >>
> >> With Regards
> >> Abhishek Acharya
> >> --
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> >>
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