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 <[email protected]>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 > > <[email protected]>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 > >> -- > >> gmx-users mailing list [email protected] > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [email protected]. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
