GROMACS version: 2020.3
GROMACS modification: No
Edit: All fixed now! I accidentally set the 2nd annealing time to the last time step instead of the last time.
I’m trying to run simulated annealing but my temperatures don’t seem to be following a linear decrease and instead are fluctuating a lot. How can I fix this? Also, what should I set ref_t to be during simulated annealing?
Here’s the start of my .log file:
> :-) GROMACS - gmx mdrun, 2020.3 (-: > > GROMACS is written by: > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen > Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd > Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray > Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang > Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis > Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson > Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund > Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall > Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov > Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen > Christian Wennberg Maarten Wolf Artem Zhmurov > and the project leaders: > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2019, The GROMACS development team at > Uppsala University, Stockholm University and > the Royal Institute of Technology, Sweden. > check out http://www.gromacs.org for more information. > > GROMACS is free software; you can redistribute it and/or modify it > under the terms of the GNU Lesser General Public License > as published by the Free Software Foundation; either version 2.1 > of the License, or (at your option) any later version. > > GROMACS: gmx mdrun, version 2020.3 > Executable: /usr/local/gromacs/bin/gmx > Data prefix: /usr/local/gromacs > Working dir: /Users/profile1/Desktop/gromacs-related_work/NPs_BBB/PS/PSNP/PSNP2 > Process ID: 12331 > Command line: > gmx mdrun -deffnm SA -v -nt 1 > > GROMACS version: 2020.3 > Verified release checksum is c0599e547549c2d0ef4fc678dc5a26ad0000eab045e938fed756f9ff5b99a197 > Precision: single > Memory model: 64 bit > MPI library: thread_mpi > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) > GPU support: OpenCL > SIMD instructions: AVX2_256 > FFT library: fftw-3.3.8-sse2 > RDTSCP usage: enabled > TNG support: enabled > Hwloc support: disabled > Tracing support: disabled > C compiler: /usr/local/bin/icc Intel 19.1.2.20200623 > C compiler flags: -march=core-avx2 -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG > C++ compiler: /usr/local/bin/icpc Intel 19.1.2.20200623 > C++ compiler flags: -march=core-avx2 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG > OpenCL include dir: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework > OpenCL library: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework > OpenCL version: 1.2 > > > Running on 1 node with total 4 cores, 4 logical cores, 0 compatible GPUs > Hardware detected: > CPU info: > Vendor: Intel > Brand: Intel(R) Core(TM) i5-4570R CPU @ 2.70GHz > Family: 6 Model: 70 Stepping: 1 > Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic > Hardware topology: Only logical processor count > GPU info: > Number of GPUs detected: 1 > #0: name: Iris Pro, vendor: Intel, device version: OpenCL 1.2 , stat: incompatible (please recompile with GMX_OPENCL_NB_CLUSTER_SIZE=4) > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. > Lindahl > GROMACS: High performance molecular simulations through multi-level > parallelism from laptops to supercomputers > SoftwareX 1 (2015) pp. 19-25 > -------- -------- --- Thank You --- -------- -------- > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl > Tackling Exascale Software Challenges in Molecular Dynamics Simulations with > GROMACS > In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 > -------- -------- --- Thank You --- -------- -------- > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. > Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl > GROMACS 4.5: a high-throughput and highly parallel open source molecular > simulation toolkit > Bioinformatics 29 (2013) pp. 845-54 > -------- -------- --- Thank You --- -------- -------- > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl > GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable > molecular simulation > J. Chem. Theory Comput. 4 (2008) pp. 435-447 > -------- -------- --- Thank You --- -------- -------- > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. > Berendsen > GROMACS: Fast, Flexible and Free > J. Comp. Chem. 26 (2005) pp. 1701-1719 > -------- -------- --- Thank You --- -------- -------- > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > E. Lindahl and B. Hess and D. van der Spoel > GROMACS 3.0: A package for molecular simulation and trajectory analysis > J. Mol. Mod. 7 (2001) pp. 306-317 > -------- -------- --- Thank You --- -------- -------- > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > H. J. C. Berendsen, D. van der Spoel and R. van Drunen > GROMACS: A message-passing parallel molecular dynamics implementation > Comp. Phys. Comm. 91 (1995) pp. 43-56 > -------- -------- --- Thank You --- -------- -------- > > > ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++ > https://doi.org/10.5281/zenodo.3923645 > -------- -------- --- Thank You --- -------- -------- > > Input Parameters: > integrator = md > tinit = 0 > dt = 0.02 > nsteps = 2500000 > init-step = 0 > simulation-part = 1 > comm-mode = Linear > nstcomm = 100 > bd-fric = 0 > ld-seed = -299389755 > emtol = 10 > emstep = 0.01 > niter = 20 > fcstep = 0 > nstcgsteep = 1000 > nbfgscorr = 10 > rtpi = 0.05 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 1000 > nstcalcenergy = 100 > nstenergy = 100 > nstxout-compressed = 1000 > compressed-x-precision = 100 > cutoff-scheme = Verlet > nstlist = 15 > pbc = xyz > periodic-molecules = false > verlet-buffer-tolerance = 0.005 > rlist = 1.1 > coulombtype = Reaction-Field > coulomb-modifier = Potential-shift > rcoulomb-switch = 0 > rcoulomb = 1.1 > epsilon-r = 15 > epsilon-rf = inf > vdw-type = Cut-off > vdw-modifier = Potential-shift > rvdw-switch = 0 > rvdw = 1.1 > DispCorr = No > table-extension = 1 > fourierspacing = 0.12 > fourier-nx = 0 > fourier-ny = 0 > fourier-nz = 0 > pme-order = 4 > ewald-rtol = 1e-05 > ewald-rtol-lj = 0.001 > lj-pme-comb-rule = Geometric > ewald-geometry = 0 > epsilon-surface = 0 > tcoupl = Nose-Hoover > nsttcouple = 15 > nh-chain-length = 1 > print-nose-hoover-chain-variables = false > pcoupl = No > pcoupltype = Isotropic > nstpcouple = -1 > tau-p = 1 > compressibility (3x3): > compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > ref-p (3x3): > ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > refcoord-scaling = No > posres-com (3): > posres-com[0]= 0.00000e+00 > posres-com[1]= 0.00000e+00 > posres-com[2]= 0.00000e+00 > posres-comB (3): > posres-comB[0]= 0.00000e+00 > posres-comB[1]= 0.00000e+00 > posres-comB[2]= 0.00000e+00 > QMMM = false > QMconstraints = 0 > QMMMscheme = 0 > MMChargeScaleFactor = 1 > qm-opts: > ngQM = 0 > constraint-algorithm = Lincs > continuation = true > Shake-SOR = false > shake-tol = 0.0001 > lincs-order = 4 > lincs-iter = 1 > lincs-warnangle = 30 > nwall = 0 > wall-type = 9-3 > wall-r-linpot = -1 > wall-atomtype[0] = -1 > wall-atomtype[1] = -1 > wall-density[0] = 0 > wall-density[1] = 0 > wall-ewald-zfac = 3 > pull = false > awh = false > rotation = false > interactiveMD = false > disre = No > disre-weighting = Conservative > disre-mixed = false > dr-fc = 1000 > dr-tau = 0 > nstdisreout = 100 > orire-fc = 0 > orire-tau = 0 > nstorireout = 100 > free-energy = no > cos-acceleration = 0 > deform (3x3): > deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > simulated-tempering = false > swapcoords = no > userint1 = 0 > userint2 = 0 > userint3 = 0 > userint4 = 0 > userreal1 = 0 > userreal2 = 0 > userreal3 = 0 > userreal4 = 0 > applied-forces: > electric-field: > x: > E0 = 0 > omega = 0 > t0 = 0 > sigma = 0 > y: > E0 = 0 > omega = 0 > t0 = 0 > sigma = 0 > z: > E0 = 0 > omega = 0 > t0 = 0 > sigma = 0 > density-guided-simulation: > active = false > group = protein > similarity-measure = inner-product > atom-spreading-weight = unity > force-constant = 1e+09 > gaussian-transform-spreading-width = 0.2 > gaussian-transform-spreading-range-in-multiples-of-width = 4 > reference-density-filename = reference.mrc > nst = 1 > normalize-densities = true > adaptive-force-scaling = false > adaptive-force-scaling-time-constant = 4 > grpopts: > nrdf: 3597 > ref-t: 400 > tau-t: 6 > annealing: Single > annealing-npoints: 2 > annealing-time [0]: 0.0 1250000.0 > annealing-temp [0]: 400.0 200.0 > acc: 0 0 0 > nfreeze: N N N > energygrp-flags[ 0]: 0 > > Changing nstlist from 15 to 50, rlist from 1.1 to 1.205 > > Using 1 MPI thread > Using 1 OpenMP thread > > System total charge: 0.000 > Reaction-Field: > epsRF = 0, rc = 1.1, krf = 0.375657, crf = 1.36364, epsfac = 9.26236 > The electrostatics potential has its minimum at r = 1.1 > Potential shift: LJ r^-12: -3.186e-01 r^-6: -5.645e-01 > > Using SIMD 4x8 nonbonded short-range kernels > > Using a dual 4x8 pair-list setup updated with dynamic pruning: > outer list: updated every 50 steps, buffer 0.105 nm, rlist 1.205 nm > inner list: updated every 33 steps, buffer 0.004 nm, rlist 1.104 nm > At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: > outer list: updated every 50 steps, buffer 0.211 nm, rlist 1.311 nm > inner list: updated every 33 steps, buffer 0.054 nm, rlist 1.154 nm > > Using full Lennard-Jones parameter combination matrix > > > Initializing LINear Constraint Solver > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > B. Hess > P-LINCS: A Parallel Linear Constraint Solver for molecular simulation > J. Chem. Theory Comput. 4 (2008) pp. 116-122 > -------- -------- --- Thank You --- -------- -------- > > The number of constraints is 1200 > 1200 constraints are involved in constraint triangles, > will apply an additional matrix expansion of order 4 for couplings > between constraints inside triangles > There are: 1600 Atoms > Center of mass motion removal mode is Linear > We have the following groups for center of mass motion removal: > 0: rest > > Started mdrun on rank 0 Sat Sep 5 18:06:21 2020 > > Step Time > 0 0.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.44396e+03 4.75099e+03 -2.23206e+04 0.00000e+00 -1.61256e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 7.68328e+03 -8.44233e+03 -8.44233e+03 5.13809e+02 -3.57386e-02 > Constr. rmsd > 1.30156e-05 > > Step Time > 1000 20.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.47773e+03 4.29683e+03 -2.24219e+04 0.00000e+00 -1.66473e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 6.74575e+03 -9.90155e+03 -7.73541e+03 4.51113e+02 -2.43294e-01 > Constr. rmsd > 9.53834e-06 > > Step Time > 2000 40.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.31959e+03 3.81602e+03 -2.32187e+04 0.00000e+00 -1.80831e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 6.01271e+03 -1.20704e+04 -6.98541e+03 4.02092e+02 -7.65389e-02 > Constr. rmsd > 8.13347e-06 > > Step Time > 3000 60.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.11215e+03 3.77865e+03 -2.37647e+04 0.00000e+00 -1.88739e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.61672e+03 -1.32572e+04 -6.32046e+03 3.75611e+02 1.72571e+00 > Constr. rmsd > 8.28727e-06 > > Step Time > 4000 80.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.05270e+03 3.60942e+03 -2.36426e+04 0.00000e+00 -1.89805e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.43226e+03 -1.35482e+04 -5.76827e+03 3.63275e+02 -2.04870e+00 > Constr. rmsd > 7.11529e-06 > > Step Time > 5000 100.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.16428e+03 3.58246e+03 -2.39778e+04 0.00000e+00 -1.92311e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.50359e+03 -1.37275e+04 -5.36259e+03 3.68046e+02 1.03050e+00 > Constr. rmsd > 7.23516e-06 > > Step Time > 6000 120.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.19378e+03 3.61724e+03 -2.35766e+04 0.00000e+00 -1.87656e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.23937e+03 -1.35262e+04 -5.07204e+03 3.50376e+02 -5.53289e-01 > Constr. rmsd > 6.82184e-06 > > Step Time > 7000 140.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.23539e+03 3.78676e+03 -2.35362e+04 0.00000e+00 -1.85140e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.64150e+03 -1.28725e+04 -4.65291e+03 3.77268e+02 -1.11789e+00 > Constr. rmsd > 7.08152e-06 > > Step Time > 8000 160.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.28060e+03 4.02801e+03 -2.29844e+04 0.00000e+00 -1.76758e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 6.24316e+03 -1.14326e+04 -4.75908e+03 4.17503e+02 6.96880e-01 > Constr. rmsd > 9.27470e-06 > > Step Time > 9000 180.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.29935e+03 4.02473e+03 -2.29541e+04 0.00000e+00 -1.76300e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 6.77080e+03 -1.08592e+04 -4.85127e+03 4.52789e+02 -9.72132e-01 > Constr. rmsd > 1.06542e-05 > > Step Time > 10000 200.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.28415e+03 3.84730e+03 -2.32077e+04 0.00000e+00 -1.80762e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.69769e+03 -1.23785e+04 -4.95573e+03 3.81025e+02 1.49824e+00 > Constr. rmsd > 7.12534e-06 > > Step Time > 11000 220.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.27041e+03 3.82537e+03 -2.34829e+04 0.00000e+00 -1.83871e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.86775e+03 -1.25194e+04 -5.03481e+03 3.92398e+02 2.52879e+00 > Constr. rmsd > 9.09290e-06 > > Step Time > 12000 240.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.11491e+03 3.82147e+03 -2.35672e+04 0.00000e+00 -1.86309e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.48923e+03 -1.31416e+04 -5.08356e+03 3.67085e+02 -1.90958e+00 > Constr. rmsd > 7.73796e-06 > > Step Time > 13000 260.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.23664e+03 3.82506e+03 -2.34781e+04 0.00000e+00 -1.84164e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.50849e+03 -1.29079e+04 -4.75688e+03 3.68373e+02 9.53551e-01 > Constr. rmsd > 7.10332e-06 > > Step Time > 14000 280.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.41071e+03 3.86086e+03 -2.30838e+04 0.00000e+00 -1.78122e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 6.52360e+03 -1.12886e+04 -4.70929e+03 4.36258e+02 -8.29381e-01 > Constr. rmsd > 8.99320e-06 > > Step Time > 15000 300.00000 > > Current ref_t for group System: 400.0 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.35228e+03 4.11305e+03 -2.30397e+04 0.00000e+00 -1.75744e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 6.63192e+03 -1.09424e+04 -4.75942e+03 4.43501e+02 1.04442e+00 > Constr. rmsd > 9.53887e-06 > > Step Time > 16000 320.00000 > > Current ref_t for group System: 399.9 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.35592e+03 4.06219e+03 -2.29018e+04 0.00000e+00 -1.74837e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 6.49538e+03 -1.09883e+04 -4.87241e+03 4.34370e+02 6.34556e-01 > Constr. rmsd > 1.03111e-05 > > Step Time > 17000 340.00000 > > Current ref_t for group System: 399.9 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.27899e+03 3.93051e+03 -2.34645e+04 0.00000e+00 -1.82550e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 6.17516e+03 -1.20799e+04 -4.85316e+03 4.12956e+02 -1.00637e+00 > Constr. rmsd > 1.03241e-05 > > Step Time > 18000 360.00000 > > Current ref_t for group System: 399.9 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.31331e+03 3.77261e+03 -2.35246e+04 0.00000e+00 -1.84387e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.97483e+03 -1.24638e+04 -4.91147e+03 3.99559e+02 -8.68265e-01 > Constr. rmsd > 9.64900e-06 > > Step Time > 19000 380.00000 > > Current ref_t for group System: 399.9 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.21508e+03 3.76006e+03 -2.35352e+04 0.00000e+00 -1.85601e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.71313e+03 -1.28469e+04 -4.92194e+03 3.82058e+02 7.41787e-01 > Constr. rmsd > 8.53789e-06 > > Step Time > 20000 400.00000 > > Current ref_t for group System: 399.9 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.20786e+03 3.68793e+03 -2.37471e+04 0.00000e+00 -1.88513e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.41134e+03 -1.34400e+04 -4.87929e+03 3.61876e+02 3.37654e+00 > Constr. rmsd > 7.71699e-06 > > Step Time > 21000 420.00000 > > Current ref_t for group System: 399.9 > > Energies (kJ/mol) > Bond Angle LJ (SR) Coulomb (SR) Potential > 1.16944e+03 3.60634e+03 -2.35745e+04 0.00000e+00 -1.87987e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 5.64993e+03 -1.31487e+04 -4.82150e+03 3.77832e+02 9.86983e-01 > Constr. rmsd > 7.39476e-06
Here’s my temperature graph:
SA-temp.xvg (390.4 KB)
Thank you in advance!