On 30/08/2012 3:43 AM, jesmin jahan wrote:
Hi Justin, Thanks a lot for your reply. I really appreciate the gromacs_user folrun help line.I see! thats why you are not receiving any attachment! My goal is to compute only GB-energy. I have computed only GB- energy using Amber and Other packages. Now I am using Gromacs to do the same. As suggested by Mark, I am usually deleting all the bonded terms for the topol.top file and also setting the non-bonded parameter values to zero in the ffnonbonded.itp file, so that other computations do not occur and the timing I get only reports that of GB- Energy.
... which is potentially reasonable only with mdrun -rerun, and IMO not useful regardless. Timings from a single step of anything are useless too. One is only interested in the time to compute things on thousands to millions of these configurations.
I have done this for different 168 protein molecules and Gromacs is performing really well and the energy values are comparable with amber and Octree based approach. However, for CMV, I am getting an energy value which is almost half of others. So, to check, now I am not excluding any bonded terms and using the original force field files provided in gromacs/share/top folder. Still the value for GB-energy is the same as before :-(.
All the energy terms look like garbage. Visualize the output of pdb2gmx and look for problems, particularly with regard to termini of distinct protein chains.
Mark
Here is the log file content (without any modification in .top file and without the mdrun-rerun command). 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: 1.5291e+06 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 Initial maximum inter charge-group distances: two-body bonded interactions: 0.425 nm, GB 1-4 Pol., atoms 24304 24312 multi-body bonded interactions: 0.425 nm, Proper Dih., atoms 24304 24312 Minimum cell size due to bonded interactions: 0.467 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 0.584 nm The maximum allowed number of cells is: X 43 Y 43 Z 43 Domain decomposition grid 4 x 2 x 2, 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 X5670 @ 2.93GHz 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: None WARNING! Binary not matching hardware - you are likely losing performance. 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: 780.000 Generated table with 1000 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ12. Tabscale = 500 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Linking all bonded interactions to atoms The initial number of communication pulses is: X 1 Y 1 Z 1 The initial domain decomposition cell size is: X 6.33 nm Y 12.66 nm Z 12.66 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) 1.000 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 Z 1 The minimum size for domain decomposition cells is 1.000 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.16 Y 0.00 Z 0.00 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) 1.000 nm Making 3D domain decomposition grid 4 x 2 x 2, 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: 509700 Atoms Charge group distribution at step 0: 31431 30755 30753 31435 33210 32021 32023 33214 32024 33215 33217 32028 30752 31434 31432 30756 Grid: 12 x 20 x 20 cells Initial temperature: 0 K Started mdrun on node 0 Wed Aug 29 09:58:13 2012 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih.GB Polarization 2.49688e+06 4.48143e+05 1.23111e+06 1.83801e+04 -2.49498e+06 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Potential 8.56489e+05 5.21939e+06 3.98993e+05 -8.11154e+06 6.28585e+04 Kinetic En. Total Energy Temperature Pressure (bar) 7.32160e+06 7.38446e+06 1.15177e+03 0.00000e+00 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 1 steps using 1 frames Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih.GB Polarization 2.49688e+06 4.48143e+05 1.23111e+06 1.83801e+04 -2.49498e+06 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Potential 8.56489e+05 5.21939e+06 3.98993e+05 -8.11154e+06 6.28585e+04 Kinetic En. Total Energy Temperature Pressure (bar) 7.32160e+06 7.38446e+06 1.15177e+03 0.00000e+00 Total Virial (kJ/mol) -1.57464e+07 5.62500e-01 -2.12500e+00 3.28125e-01 -1.57464e+07 3.25000e+00 -3.67188e+00 -2.68750e+00 -1.57464e+07 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) 9.76562e-04 0.00000e+00 1.95312e-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 1.626204 78.058 0.3 GB Coulomb + LJ 73.629096 4491.375 17.3 Outer nonbonded loop 1.962706 19.627 0.1 1,4 nonbonded interactions 1.348860 121.397 0.5 Born radii (HCT/OBC) 78.053220 14283.739 55.0 Born force chain rule 78.053220 1170.798 4.5 NS-Pairs 245.058526 5146.229 19.8 Reset In Box 0.509700 1.529 0.0 CG-CoM 1.019400 3.058 0.0 Bonds 0.514800 30.373 0.1 Angles 0.934260 156.956 0.6 Propers 1.742760 399.092 1.5 Virial 0.510420 9.188 0.0 Stop-CM 1.019400 10.194 0.0 Calc-Ekin 1.019400 27.524 0.1 ----------------------------------------------------------------------------- Total 25949.137 100.0 ----------------------------------------------------------------------------- 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 103046.0 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 2.870 2.0 0.7 Comm. coord. 16 1 0.943 0.6 0.2 Neighbor search 16 1 20.102 13.7 5.0 Force 16 1 132.542 90.4 32.7 Wait + Comm. F 16 1 2.315 1.6 0.6 Update 16 1 0.130 0.1 0.0 Comm. energies 16 1 0.090 0.1 0.0 Rest 16 246.272 167.9 60.8 ----------------------------------------------------------------------- Total 16 405.265 276.3 100.0 ----------------------------------------------------------------------- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 8.635 8.635 100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 8.715 3.005 0.010 2398.708 Finished mdrun on node 0 Wed Aug 29 09:58:22 2012 Thanks, Jesmin On Wed, Aug 29, 2012 at 1:11 PM, Justin Lemkul <jalem...@vt.edu> wrote:On 8/29/12 1:06 PM, jesmin jahan wrote:Dear Justin, Thanks for your reply. Here is the CMV.log file . Please check it.What you've posted is output from grompp. Note that if you're trying to send attachments, the list rejects them.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.Something doesn't add up. The energy values were indicative of a completely unphysical system.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.For a single-point energy evaluation this probably isn't significant.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-zeroFinite cutoffs do have a significant outcome of implicit calculations, but if you're doing this to remain consistent with other software, I suppose you have to keep them as they are.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.How are you excluding bonded terms? If you're hacking the topology to remove the bonds, you're going to get a bunch of junk. I haven't followed this entire thread fully, but if you're trying to just get certain energies and not others, that's what mdrun -rerun is for. You don't initiate an mdrun with a broken physical model, otherwise the output will be nonsense. -JustinThanks, 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. -JustinThanks, 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-- ======================================== 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
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