[gmx-users] High Temperatures in NVT

Abhishek Acharya aacharya at iitk.ac.in
Fri Mar 15 11:02:52 CET 2013


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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