Dear Justin, Thanks for your reply. Here is the CMV.log file . Please check it.
Actually, the .pdb file I am using is already minimized and we are using the same file for amber 11 and Octree based molecular dynamic package. I will also do the minimization step to see what happens. One thing I also want to mention is when I run grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr command, I get following the log. NOTE 1 [file mdr.mdp]: Tumbling and or flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR. NOTE 2 [file mdr.mdp]: You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = Shift (possibly with DispCorr) NOTE 3 [file mdr.mdp]: You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = PME-Switch or Reaction-Field-zero NOTE 4 [file mdr.mdp]: No SA (non-polar) calculation requested together with GB. Are you sure this is what you want? Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Excluding 3 bonded neighbours molecule type 'Protein_chain_C' Excluding 3 bonded neighbours molecule type 'Protein_chain_A2' Excluding 3 bonded neighbours molecule type 'Protein_chain_B2' Excluding 3 bonded neighbours molecule type 'Protein_chain_C2' Excluding 3 bonded neighbours molecule type 'Protein_chain_A3' Excluding 3 bonded neighbours molecule type 'Protein_chain_B3' Excluding 3 bonded neighbours molecule type 'Protein_chain_C3' Excluding 3 bonded neighbours molecule type 'Protein_chain_A4' Excluding 3 bonded neighbours molecule type 'Protein_chain_B4' Excluding 3 bonded neighbours molecule type 'Protein_chain_C4' Excluding 3 bonded neighbours molecule type 'Protein_chain_A5' Excluding 3 bonded neighbours molecule type 'Protein_chain_B5' Excluding 3 bonded neighbours molecule type 'Protein_chain_C5' Excluding 3 bonded neighbours molecule type 'Protein_chain_A6' Excluding 3 bonded neighbours molecule type 'Protein_chain_B6' Excluding 3 bonded neighbours molecule type 'Protein_chain_C6' Excluding 3 bonded neighbours molecule type 'Protein_chain_A7' Excluding 3 bonded neighbours molecule type 'Protein_chain_B7' Excluding 3 bonded neighbours molecule type 'Protein_chain_C7' Excluding 3 bonded neighbours molecule type 'Protein_chain_A8' Excluding 3 bonded neighbours molecule type 'Protein_chain_B8' Excluding 3 bonded neighbours molecule type 'Protein_chain_C8' Excluding 3 bonded neighbours molecule type 'Protein_chain_A9' Excluding 3 bonded neighbours molecule type 'Protein_chain_B9' Excluding 3 bonded neighbours molecule type 'Protein_chain_C9' Excluding 3 bonded neighbours molecule type 'Protein_chain_A10' Excluding 3 bonded neighbours molecule type 'Protein_chain_B10' Excluding 3 bonded neighbours molecule type 'Protein_chain_C10' Excluding 3 bonded neighbours molecule type 'Protein_chain_A11' Excluding 3 bonded neighbours molecule type 'Protein_chain_B11' Excluding 3 bonded neighbours molecule type 'Protein_chain_C11' Excluding 3 bonded neighbours molecule type 'Protein_chain_A12' Excluding 3 bonded neighbours molecule type 'Protein_chain_B12' Excluding 3 bonded neighbours molecule type 'Protein_chain_C12' Excluding 3 bonded neighbours molecule type 'Protein_chain_A13' Excluding 3 bonded neighbours molecule type 'Protein_chain_B13' Excluding 3 bonded neighbours molecule type 'Protein_chain_C13' Excluding 3 bonded neighbours molecule type 'Protein_chain_A14' Excluding 3 bonded neighbours molecule type 'Protein_chain_B14' Excluding 3 bonded neighbours molecule type 'Protein_chain_C14' Excluding 3 bonded neighbours molecule type 'Protein_chain_A15' Excluding 3 bonded neighbours molecule type 'Protein_chain_B15' Excluding 3 bonded neighbours molecule type 'Protein_chain_C15' Excluding 3 bonded neighbours molecule type 'Protein_chain_A16' Excluding 3 bonded neighbours molecule type 'Protein_chain_B16' Excluding 3 bonded neighbours molecule type 'Protein_chain_C16' Excluding 3 bonded neighbours molecule type 'Protein_chain_A17' Excluding 3 bonded neighbours molecule type 'Protein_chain_B17' Excluding 3 bonded neighbours molecule type 'Protein_chain_C17' Excluding 3 bonded neighbours molecule type 'Protein_chain_A18' Excluding 3 bonded neighbours molecule type 'Protein_chain_B18' Excluding 3 bonded neighbours molecule type 'Protein_chain_C18' Excluding 3 bonded neighbours molecule type 'Protein_chain_A19' Excluding 3 bonded neighbours molecule type 'Protein_chain_B19' Excluding 3 bonded neighbours molecule type 'Protein_chain_C19' Excluding 3 bonded neighbours molecule type 'Protein_chain_A20' Excluding 3 bonded neighbours molecule type 'Protein_chain_B20' Excluding 3 bonded neighbours molecule type 'Protein_chain_C20' Excluding 3 bonded neighbours molecule type 'Protein_chain_A21' Excluding 3 bonded neighbours molecule type 'Protein_chain_B21' Excluding 3 bonded neighbours molecule type 'Protein_chain_C21' Excluding 3 bonded neighbours molecule type 'Protein_chain_A22' Excluding 3 bonded neighbours molecule type 'Protein_chain_B22' Excluding 3 bonded neighbours molecule type 'Protein_chain_C22' Excluding 3 bonded neighbours molecule type 'Protein_chain_A23' Excluding 3 bonded neighbours molecule type 'Protein_chain_B23' Excluding 3 bonded neighbours molecule type 'Protein_chain_C23' Excluding 3 bonded neighbours molecule type 'Protein_chain_A24' Excluding 3 bonded neighbours molecule type 'Protein_chain_B24' Excluding 3 bonded neighbours molecule type 'Protein_chain_C24' Excluding 3 bonded neighbours molecule type 'Protein_chain_A25' Excluding 3 bonded neighbours molecule type 'Protein_chain_B25' Excluding 3 bonded neighbours molecule type 'Protein_chain_C25' Excluding 3 bonded neighbours molecule type 'Protein_chain_A26' Excluding 3 bonded neighbours molecule type 'Protein_chain_B26' Excluding 3 bonded neighbours molecule type 'Protein_chain_C26' Excluding 3 bonded neighbours molecule type 'Protein_chain_A27' Excluding 3 bonded neighbours molecule type 'Protein_chain_B27' Excluding 3 bonded neighbours molecule type 'Protein_chain_C27' Excluding 3 bonded neighbours molecule type 'Protein_chain_A28' Excluding 3 bonded neighbours molecule type 'Protein_chain_B28' Excluding 3 bonded neighbours molecule type 'Protein_chain_C28' Excluding 3 bonded neighbours molecule type 'Protein_chain_A29' Excluding 3 bonded neighbours molecule type 'Protein_chain_B29' Excluding 3 bonded neighbours molecule type 'Protein_chain_C29' Excluding 3 bonded neighbours molecule type 'Protein_chain_A30' Excluding 3 bonded neighbours molecule type 'Protein_chain_B30' Excluding 3 bonded neighbours molecule type 'Protein_chain_C30' Excluding 3 bonded neighbours molecule type 'Protein_chain_A31' Excluding 3 bonded neighbours molecule type 'Protein_chain_B31' Excluding 3 bonded neighbours molecule type 'Protein_chain_C31' Excluding 3 bonded neighbours molecule type 'Protein_chain_A32' Excluding 3 bonded neighbours molecule type 'Protein_chain_B32' Excluding 3 bonded neighbours molecule type 'Protein_chain_C32' Excluding 3 bonded neighbours molecule type 'Protein_chain_A33' Excluding 3 bonded neighbours molecule type 'Protein_chain_B33' Excluding 3 bonded neighbours molecule type 'Protein_chain_C33' Excluding 3 bonded neighbours molecule type 'Protein_chain_A34' Excluding 3 bonded neighbours molecule type 'Protein_chain_B34' Excluding 3 bonded neighbours molecule type 'Protein_chain_C34' Excluding 3 bonded neighbours molecule type 'Protein_chain_A35' Excluding 3 bonded neighbours molecule type 'Protein_chain_B35' Excluding 3 bonded neighbours molecule type 'Protein_chain_C35' ... so on. NOTE 5 [file topol.top, line 388]: System has non-zero total charge: 780.000004 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Analysing residue names: There are: 32280 Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 1529097.00 This run will generate roughly 39 Mb of data There were 5 notes Back Off! I just backed up imd.tpr to ./#imd.tpr.1# gcq#97: "The Universe is Somewhere In Here" (J.G.E.M. Fraaije) I was only interested in non bonded terms (Specially GB-Energy), so I guess, exclusion of bonded terms is not a problem. Thanks, Jesmin On Wed, Aug 29, 2012 at 12:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/29/12 11:27 AM, jesmin jahan wrote: >> >> Ops! >> >> Thanks Justin for you quick reply. >> Sorry, I have attached a log file from previous run. I am attaching >> the correct log file here. Please have a look. >> > > I don't see a new .log file attached anywhere. > > >> Actually, I am a Computer Science student. I do not have enough >> background of Molecular Dynamics. >> I am using these three commands and >> >> pdb2gmx -f 1F15-full.pdb -ter -ignh -ff amber99 -water none >> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr >> OMP_NUM_THREADS=12 mdrun -nt 16 -s imd.tpr >> >> and my .mdp file is like this: >> >> constraints = none >> integrator = md >> pbc = no >> dt = 0.001 ; ps >> nsteps = 0 ; 100000 ps = 100 ns >> rcoulomb = 1 >> rvdw = 1 >> rlist =1 >> nstgbradii = 1 >> rgbradii = 1 >> implicit_solvent = GBSA >> gb_algorithm = HCT ; OBC ; Still >> sa_algorithm = None >> >> >> What else might go wrong? >> > > The normal workflow included energy minimization before running MD. Basic > tutorial material covers this. Without EM, you assume that whatever > structure you're using is suitable for MD, which may or may not be true. > > -Justin > > >> Thanks, >> Jesmin >> >> On Wed, Aug 29, 2012 at 11:14 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 8/29/12 11:11 AM, jesmin jahan wrote: >>>> >>>> >>>> Thanks Mark for your reply. >>>> >>>> For the time being, I admit your claim that I am comparing apple with >>>> orange. >>>> So, to investigate more, I run the simulation without any modification >>>> in parameter fields and force field I am using. My test data is CMV >>>> virus shell. >>>> I am using the following commands. >>>> >>>> pdb2gmx -f 1F15-full.pdb -ter -ignh -ff amber99 -water none >>>> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr >>>> OMP_NUM_THREADS=12 mdrun -nt 16 -s imd.tpr >>>> >>>> >>>> The log file looks like this: >>>> :-) G R O M A C S (-: >>>> >>>> GROningen MAchine for Chemical Simulation >>>> >>>> :-) VERSION 4.6-dev-20120820-87e5bcf (-: >>>> >>>> Written by Emile Apol, Rossen Apostolov, Herman J.C. >>>> Berendsen, >>>> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton >>>> Feenstra, >>>> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, >>>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, >>>> Michael Shirts, Alfons Sijbers, Peter Tieleman, >>>> >>>> Berk Hess, David van der Spoel, and Erik Lindahl. >>>> >>>> Copyright (c) 1991-2000, University of Groningen, The >>>> Netherlands. >>>> Copyright (c) 2001-2010, The GROMACS development team at >>>> Uppsala University & The Royal Institute of Technology, >>>> Sweden. >>>> check out http://www.gromacs.org for more information. >>>> >>>> This program is free software; you can redistribute it and/or >>>> modify it under the terms of the GNU General Public License >>>> as published by the Free Software Foundation; either version >>>> 2 >>>> of the License, or (at your option) any later version. >>>> >>>> :-) mdrun_mpi (-: >>>> >>>> >>>> ++++ 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 --- -------- -------- >>>> >>>> Input Parameters: >>>> integrator = md >>>> nsteps = 0 >>>> init-step = 0 >>>> ns-type = Grid >>>> nstlist = 10 >>>> ndelta = 2 >>>> nstcomm = 10 >>>> comm-mode = Linear >>>> nstlog = 1000 >>>> nstxout = 0 >>>> nstvout = 0 >>>> nstfout = 0 >>>> nstcalcenergy = 10 >>>> nstenergy = 100 >>>> nstxtcout = 0 >>>> init-t = 0 >>>> delta-t = 0.001 >>>> xtcprec = 1000 >>>> nkx = 0 >>>> nky = 0 >>>> nkz = 0 >>>> pme-order = 4 >>>> ewald-rtol = 1e-05 >>>> ewald-geometry = 0 >>>> epsilon-surface = 0 >>>> optimize-fft = FALSE >>>> ePBC = no >>>> bPeriodicMols = FALSE >>>> bContinuation = FALSE >>>> bShakeSOR = FALSE >>>> etc = No >>>> bPrintNHChains = FALSE >>>> nsttcouple = -1 >>>> epc = No >>>> epctype = Isotropic >>>> nstpcouple = -1 >>>> tau-p = 1 >>>> 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} >>>> compress (3x3): >>>> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >>>> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >>>> compress[ 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 >>>> rlist = 1 >>>> rlistlong = 1 >>>> rtpi = 0.05 >>>> coulombtype = Cut-off >>>> rcoulomb-switch = 0 >>>> rcoulomb = 1 >>>> vdwtype = Cut-off >>>> rvdw-switch = 0 >>>> rvdw = 1 >>>> epsilon-r = 1 >>>> epsilon-rf = inf >>>> tabext = 1 >>>> implicit-solvent = GBSA >>>> gb-algorithm = HCT >>>> gb-epsilon-solvent = 80 >>>> nstgbradii = 1 >>>> rgbradii = 1 >>>> gb-saltconc = 0 >>>> gb-obc-alpha = 1 >>>> gb-obc-beta = 0.8 >>>> gb-obc-gamma = 4.85 >>>> gb-dielectric-offset = 0.009 >>>> sa-algorithm = None >>>> sa-surface-tension = 2.25936 >>>> DispCorr = No >>>> bSimTemp = FALSE >>>> free-energy = no >>>> nwall = 0 >>>> wall-type = 9-3 >>>> wall-atomtype[0] = -1 >>>> wall-atomtype[1] = -1 >>>> wall-density[0] = 0 >>>> wall-density[1] = 0 >>>> wall-ewald-zfac = 3 >>>> pull = no >>>> rotation = FALSE >>>> disre = No >>>> disre-weighting = Conservative >>>> disre-mixed = FALSE >>>> dr-fc = 1000 >>>> dr-tau = 0 >>>> nstdisreout = 100 >>>> orires-fc = 0 >>>> orires-tau = 0 >>>> nstorireout = 100 >>>> dihre-fc = 0 >>>> em-stepsize = 0.01 >>>> em-tol = 10 >>>> niter = 20 >>>> fc-stepsize = 0 >>>> nstcgsteep = 1000 >>>> nbfgscorr = 10 >>>> ConstAlg = Lincs >>>> shake-tol = 0.0001 >>>> lincs-order = 4 >>>> lincs-warnangle = 30 >>>> lincs-iter = 1 >>>> bd-fric = 0 >>>> ld-seed = 1993 >>>> cos-accel = 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} >>>> adress = FALSE >>>> userint1 = 0 >>>> userint2 = 0 >>>> userint3 = 0 >>>> userint4 = 0 >>>> userreal1 = 0 >>>> userreal2 = 0 >>>> userreal3 = 0 >>>> userreal4 = 0 >>>> grpopts: >>>> nrdf: 9534 >>>> ref-t: 0 >>>> tau-t: 0 >>>> anneal: No >>>> ann-npoints: 0 >>>> acc: 0 0 0 >>>> nfreeze: N N N >>>> energygrp-flags[ 0]: 0 >>>> efield-x: >>>> n = 0 >>>> efield-xt: >>>> n = 0 >>>> efield-y: >>>> n = 0 >>>> efield-yt: >>>> n = 0 >>>> efield-z: >>>> n = 0 >>>> efield-zt: >>>> n = 0 >>>> bQMMM = FALSE >>>> QMconstraints = 0 >>>> QMMMscheme = 0 >>>> scalefactor = 1 >>>> qm-opts: >>>> ngQM = 0 >>>> >>>> Initializing Domain Decomposition on 16 nodes >>>> Dynamic load balancing: auto >>>> Will sort the charge groups at every domain (re)decomposition >>>> Minimum cell size due to bonded interactions: 0.000 nm >>>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 >>>> Optimizing the DD grid for 16 cells with a minimum initial size of 0.000 >>>> nm >>>> Domain decomposition grid 4 x 4 x 1, separate PME nodes 0 >>>> Domain decomposition nodeid 0, coordinates 0 0 0 >>>> >>>> Detecting CPU-specific acceleration. Present hardware specification: >>>> Vendor: GenuineIntel >>>> Brand: Intel(R) Xeon(R) CPU X5680 @ 3.33GHz >>>> Family: 6 Model: 44 Stepping: 2 >>>> Features: htt sse2 sse4.1 aes rdtscp >>>> Acceleration most likely to fit this hardware: SSE4.1 >>>> Acceleration selected at Gromacs compile time: SSE4.1 >>>> >>>> Table routines are used for coulomb: FALSE >>>> Table routines are used for vdw: FALSE >>>> Cut-off's: NS: 1 Coulomb: 1 LJ: 1 >>>> System total charge: 6.000 >>>> Configuring nonbonded kernels... >>>> Configuring standard C nonbonded kernels... >>>> >>>> >>>> >>>> Linking all bonded interactions to atoms >>>> >>>> The initial number of communication pulses is: X 2 Y 2 >>>> The initial domain decomposition cell size is: X 0.79 nm Y 0.89 nm >>>> >>>> The maximum allowed distance for charge groups involved in interactions >>>> is: >>>> non-bonded interactions 1.000 nm >>>> (the following are initial values, they could change due to box >>>> deformation) >>>> two-body bonded interactions (-rdd) 1.000 nm >>>> multi-body bonded interactions (-rdd) 0.794 nm >>>> >>>> When dynamic load balancing gets turned on, these settings will change >>>> to: >>>> The maximum number of communication pulses is: X 2 Y 2 >>>> The minimum size for domain decomposition cells is 0.500 nm >>>> The requested allowed shrink of DD cells (option -dds) is: 0.80 >>>> The allowed shrink of domain decomposition cells is: X 0.63 Y 0.56 >>>> The maximum allowed distance for charge groups involved in interactions >>>> is: >>>> non-bonded interactions 1.000 nm >>>> two-body bonded interactions (-rdd) 1.000 nm >>>> multi-body bonded interactions (-rdd) 0.500 nm >>>> >>>> >>>> Making 2D domain decomposition grid 4 x 4 x 1, home cell index 0 0 0 >>>> >>>> Center of mass motion removal mode is Linear >>>> We have the following groups for center of mass motion removal: >>>> 0: rest >>>> There are: 3179 Atoms >>>> Charge group distribution at step 0: 84 180 252 196 237 210 255 157 >>>> 254 197 266 176 186 104 224 201 >>>> Grid: 4 x 4 x 4 cells >>>> Initial temperature: 0 K >>>> >>>> Started mdrun on node 0 Wed Aug 29 02:32:21 2012 >>>> >>>> Step Time Lambda >>>> 0 0.00000 0.00000 >>>> >>>> Energies (kJ/mol) >>>> GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic >>>> En. >>>> -1.65116e+04 5.74908e+08 -2.37699e+05 5.74654e+08 >>>> 6.36009e+11 >>>> Total Energy Temperature Pressure (bar) >>>> 6.36584e+11 1.60465e+10 0.00000e+00 >>>> >>>> <====== ############### ==> >>>> <==== A V E R A G E S ====> >>>> <== ############### ======> >>>> >>>> Statistics over 1 steps using 1 frames >>>> >>>> Energies (kJ/mol) >>>> GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic >>>> En. >>>> -1.65116e+04 5.74908e+08 -2.37699e+05 5.74654e+08 >>>> 6.36009e+11 >>>> Total Energy Temperature Pressure (bar) >>>> 6.36584e+11 1.60465e+10 0.00000e+00 >>>> >>>> Total Virial (kJ/mol) >>>> -1.13687e+09 1.14300e+07 -1.23884e+07 >>>> 1.14273e+07 -1.15125e+09 -5.31658e+06 >>>> -1.23830e+07 -5.31326e+06 -1.16512e+09 >>>> >>>> Pressure (bar) >>>> 0.00000e+00 0.00000e+00 0.00000e+00 >>>> 0.00000e+00 0.00000e+00 0.00000e+00 >>>> 0.00000e+00 0.00000e+00 0.00000e+00 >>>> >>>> Total Dipole (D) >>>> 1.35524e+03 -4.39059e+01 2.16985e+03 >>>> >>>> >>>> M E G A - F L O P S A C C O U N T I N G >>>> >>>> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy >>>> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs) >>>> NF=No Forces >>>> >>>> Computing: M-Number M-Flops % >>>> Flops >>>> >>>> >>>> ----------------------------------------------------------------------------- >>>> Generalized Born Coulomb 0.006162 0.296 >>>> 0.2 >>>> GB Coulomb + LJ 0.446368 27.228 >>>> 19.8 >>>> Outer nonbonded loop 0.015554 0.156 >>>> 0.1 >>>> Born radii (HCT/OBC) 0.452530 82.813 >>>> 60.3 >>>> Born force chain rule 0.452530 6.788 >>>> 4.9 >>>> NS-Pairs 0.940291 19.746 >>>> 14.4 >>>> Reset In Box 0.003179 0.010 >>>> 0.0 >>>> CG-CoM 0.006358 0.019 >>>> 0.0 >>>> Virial 0.003899 0.070 >>>> 0.1 >>>> Stop-CM 0.006358 0.064 >>>> 0.0 >>>> Calc-Ekin 0.006358 0.172 >>>> 0.1 >>>> >>>> >>>> ----------------------------------------------------------------------------- >>>> Total 137.361 >>>> 100.0 >>>> >>>> >>>> ----------------------------------------------------------------------------- >>>> >>>> >>>> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S >>>> >>>> av. #atoms communicated per step for force: 2 x 7369.0 >>>> >>>> >>>> R E A L C Y C L E A N D T I M E A C C O U N T I N G >>>> >>>> Computing: Nodes Number G-Cycles Seconds % >>>> ----------------------------------------------------------------------- >>>> Domain decomp. 16 1 0.210 0.1 11.4 >>>> Comm. coord. 16 1 0.006 0.0 0.3 >>>> Neighbor search 16 1 0.118 0.1 6.4 >>>> Force 16 1 1.319 0.8 71.4 >>>> Wait + Comm. F 16 1 0.016 0.0 0.9 >>>> Update 16 1 0.003 0.0 0.2 >>>> Comm. energies 16 1 0.093 0.1 5.0 >>>> Rest 16 0.082 0.1 4.4 >>>> ----------------------------------------------------------------------- >>>> Total 16 1.847 1.1 100.0 >>>> ----------------------------------------------------------------------- >>>> >>>> NOTE: 5 % of the run time was spent communicating energies, >>>> you might want to use the -gcom option of mdrun >>>> >>>> >>>> Parallel run - timing based on wallclock. >>>> >>>> NODE (s) Real (s) (%) >>>> Time: 0.036 0.036 100.0 >>>> (Mnbf/s) (GFlops) (ns/day) (hour/ns) >>>> Performance: 12.702 3.856 2.425 9.896 >>>> Finished mdrun on node 0 Wed Aug 29 02:32:21 2012 >>>> >>>> >>>> >>>> The GB- energy value reported is half of that reported by Amber 11 and >>>> Octree based Molecular dynamic package. >>>> >>>> Although I guess the difference can be due to the difference in >>>> algorithms they are using, but there could be some other reason. >>>> If anyone knows what are the possible reasons behind this, please let >>>> me know. May be fixing them will give me same value for all different >>>> Molecular Dynamic Package. >>>> >>> >>> I wouldn't trust the result you're getting here - the energy values and >>> temperature (10^10, yikes!) suggest there is something very wrong with >>> the >>> starting configuration. >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > ------ jesmin
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