Run PLL1 more em.

mdp ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no [noi@tubgrew-grid PLL1]$ grompp -v -f em -c b4em -p lys11 -o em :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, 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. :-) grompp (-: Option Filename Type Description ------------------------------------------------------------f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c b4em.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml

conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -deshuf deshuf.ndx Output, Opt. Index file -p lys11.top Input Topology file -pp processed.top Output, Opt. Topology file -o em.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description ------------------------------------------------------[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 141 of the 1176 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 2 bonded neighbours for SOL 886 NOTE: System has non-zero total charge: 1.000000e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 15 # G96ANGLES: 22

-r

# PDIHS: 7 # IDIHS: 2 # LJ14: 18 # SETTLE: 886 initialising group options... processing index file... Analysing residue names: Opening library file /opt/Bio/gromacs/share/gromacs/top/aminoacids.dat There are: 886 OTHER residues There are: 1 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for T-Coupling containing 2674 elements Making dummy/rest group for Acceleration containing 2674 elements Making dummy/rest group for Freeze containing 2674 elements Making dummy/rest group for Energy Mon. containing 2674 elements Making dummy/rest group for VCM containing 2674 elements Number of degrees of freedom in T-Coupling group rest is 5361.00 Making dummy/rest group for User1 containing 2674 elements Making dummy/rest group for User2 containing 2674 elements Making dummy/rest group for XTC containing 2674 elements Making dummy/rest group for Or. Res. Fit containing 2674 elements Making dummy/rest group for QMMM containing 2674 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... writing run input file... gcq#133: "You Will Be Surprised At What Resides In Your Inside" (Arrested Development) [noi@tubgrew-grid PLL1]$ genion -s em -o b4em -np 60 -pname NA -pq 1 -nn 60 -nname CL -nq -1 random :-) G R O M A C S (-: Green Red Orange Magenta Azure Cyan Skyblue :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, 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. :-) genion (-: Option Filename Type Description ------------------------------------------------------------s em.tpr Input Generic run input: tpr tpb tpa xml -table table.xvg Input, Opt. xvgr/xmgr file -n index.ndx Input, Opt. Index file -o b4em.gro Output Generic structure: gro g96 pdb xml -g genion.log Output Log file -pot pot.pdb Output, Opt. Protein data bank file -p topol.top In/Out, Opt. Topology file Option Type Value Description ------------------------------------------------------[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 19 Set the nicelevel -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -np int 60 Number of positive ions -pname string NA Name of the positive ion -pq int 1 Charge of the positive ion -nn int 60 Number of negative ions -nname string CL Name of the negative ion -nq int -1 Charge of the negative ion -rmin real 0.6 Minimum distance between ions -[no]random bool yes Use random placement of ions instead of based on potential. The rmin option should still work -seed int 1993 Seed for random number generator -scale real 0.001 Scaling factor for the potential for -pot -conc real 0 Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input tpr file. Overrides the -np and nn options. -[no]neutral bool no This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. ------------------------------------------------------Program genion, VERSION 3.3.1 Source code file: statutil.c, line: 799 Invalid command line argument: random

------------------------------------------------------"Ich Bin Ein Berliner" (J.F. Kennedy) [noi@tubgrew-grid PLL1]$ grompp -v -f em -c b4em -p lys11 -o em :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, 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. :-) grompp (-: Option Filename Type Description ------------------------------------------------------------f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c b4em.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -deshuf deshuf.ndx Output, Opt. Index file -p lys11.top Input Topology file -pp processed.top Output, Opt. Topology file -o em.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description ------------------------------------------------------[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate

-[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 141 of the 1176 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 2 bonded neighbours for SOL 886 NOTE: System has non-zero total charge: 1.000000e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 15 # G96ANGLES: 22 # PDIHS: 7 # IDIHS: 2 # LJ14: 18 # SETTLE: 886 initialising group options... processing index file... Analysing residue names: Opening library file /opt/Bio/gromacs/share/gromacs/top/aminoacids.dat There are: 886 OTHER residues There are: 1 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for T-Coupling containing 2674 elements Making dummy/rest group for Acceleration containing 2674 elements Making dummy/rest group for Freeze containing 2674 elements Making dummy/rest group for Energy Mon. containing 2674 elements Making dummy/rest group for VCM containing 2674 elements Number of degrees of freedom in T-Coupling group rest is 5361.00 Making dummy/rest group for User1 containing 2674 elements Making dummy/rest group for User2 containing 2674 elements Making dummy/rest group for XTC containing 2674 elements

Making dummy/rest group for Or. Res. Fit containing 2674 elements Making dummy/rest group for QMMM containing 2674 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... writing run input file... Back Off! I just backed up em.tpr to ./#em.tpr.1# gcq#289: "Do You Have a Mind of Your Own ?" (Garbage) [noi@tubgrew-grid PLL1]$ mdrun -v -s em -o em -c after_em -g emlog NNODES=1, MYRANK=0, HOSTNAME=tubgrew-grid.su.ac.th :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, 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 (-: Option Filename Type Description ------------------------------------------------------------s em.tpr Input Generic run input: tpr tpb tpa xml -o em.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_em.gro Output Generic structure: gro g96 pdb xml -e ener.edr Output Generic energy: edr ene -g emlog.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file -field field.xvg Output, Opt. xvgr/xmgr file -table table.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file

-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.xvg Output, Opt. xvgr/xmgr file -ei sam.edi Input, Opt. ED sampling input -eo sam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jo bam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description ------------------------------------------------------[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 19 Set the nicelevel -deffnm string Set the default filename for all file options -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -replex int 0 Attempt replica exchange every # steps -reseed int -1 Seed for replica exchange, -1 is generate a seed -[no]glas bool no Do glass simulation with special long range corrections -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system Getting Loaded... Reading file em.tpr, VERSION 3.3.1 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 2.00000e+03 Number of steps = 100 Step= 0, Dmax= 1.0e-02 nm, Epot= -2.09178e+04 Fmax= 1.43495e+04, atom= 377 Step= 1, Dmax= 1.0e-02 nm, Epot= -2.41771e+04 Fmax= 5.86397e+03, atom= 2453 Step= 2, Dmax= 1.2e-02 nm, Epot= -2.74830e+04 Fmax= 3.01053e+03, atom= 284 Step= 3, Dmax= 1.4e-02 nm, Epot= -3.01557e+04 Fmax= 4.10414e+03, atom= 14 Step= 4, Dmax= 1.7e-02 nm, Epot= -3.10813e+04 Fmax= 1.34891e+04, atom= 14

Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step= Step=

5, Dmax= 2.1e-02 nm, Epot= -3.16107e+04 Fmax= 7.24579e+03, atom= 10 6, Dmax= 2.5e-02 nm, Epot= -3.17229e+04 Fmax= 1.84939e+04, atom= 10 7, Dmax= 3.0e-02 nm, Epot= -3.22950e+04 Fmax= 1.24805e+04, atom= 10 9, Dmax= 1.8e-02 nm, Epot= -3.28179e+04 Fmax= 6.86057e+03, atom= 14 10, Dmax= 2.1e-02 nm, Epot= -3.30386e+04 Fmax= 1.84638e+04, atom= 14 11, Dmax= 2.6e-02 nm, Epot= -3.33880e+04 Fmax= 1.18307e+04, atom= 14 12, Dmax= 3.1e-02 nm, Epot= -3.34308e+04 Fmax= 2.37960e+04, atom= 14 13, Dmax= 3.7e-02 nm, Epot= -3.37204e+04 Fmax= 1.75853e+04, atom= 14 15, Dmax= 2.2e-02 nm, Epot= -3.41024e+04 Fmax= 4.28236e+03, atom= 14 17, Dmax= 1.3e-02 nm, Epot= -3.43399e+04 Fmax= 1.10087e+04, atom= 14 18, Dmax= 1.6e-02 nm, Epot= -3.45293e+04 Fmax= 8.28087e+03, atom= 14 19, Dmax= 1.9e-02 nm, Epot= -3.46343e+04 Fmax= 1.41087e+04, atom= 14 20, Dmax= 2.3e-02 nm, Epot= -3.47966e+04 Fmax= 1.25558e+04, atom= 14 21, Dmax= 2.8e-02 nm, Epot= -3.48128e+04 Fmax= 1.88968e+04, atom= 14 22, Dmax= 3.3e-02 nm, Epot= -3.49476e+04 Fmax= 1.80774e+04, atom= 14 24, Dmax= 2.0e-02 nm, Epot= -3.53007e+04 Fmax= 3.87034e+03, atom= 14 26, Dmax= 1.2e-02 nm, Epot= -3.54518e+04 Fmax= 1.03007e+04, atom= 14 27, Dmax= 1.4e-02 nm, Epot= -3.55955e+04 Fmax= 6.99173e+03, atom= 14 28, Dmax= 1.7e-02 nm, Epot= -3.56504e+04 Fmax= 1.36182e+04, atom= 14 29, Dmax= 2.1e-02 nm, Epot= -3.57914e+04 Fmax= 1.07662e+04, atom= 14 31, Dmax= 1.2e-02 nm, Epot= -3.59471e+04 Fmax= 3.27995e+03, atom= 14 32, Dmax= 1.5e-02 nm, Epot= -3.60488e+04 Fmax= 1.48388e+04, atom= 14 33, Dmax= 1.8e-02 nm, Epot= -3.62468e+04 Fmax= 6.99895e+03, atom= 14 35, Dmax= 1.1e-02 nm, Epot= -3.63428e+04 Fmax= 5.49494e+03, atom= 14 36, Dmax= 1.3e-02 nm, Epot= -3.64156e+04 Fmax= 9.80599e+03, atom= 14 37, Dmax= 1.5e-02 nm, Epot= -3.65101e+04 Fmax= 8.38740e+03, atom= 14 38, Dmax= 1.9e-02 nm, Epot= -3.65313e+04 Fmax= 1.34818e+04, atom= 14 39, Dmax= 2.2e-02 nm, Epot= -3.66221e+04 Fmax= 1.23391e+04, atom= 14 41, Dmax= 1.3e-02 nm, Epot= -3.67828e+04 Fmax= 2.86745e+03, atom= 14 42, Dmax= 1.6e-02 nm, Epot= -3.68131e+04 Fmax= 1.73442e+04, atom= 14 43, Dmax= 1.9e-02 nm, Epot= -3.70510e+04 Fmax= 6.90319e+03, atom= 14 45, Dmax= 1.2e-02 nm, Epot= -3.71104e+04 Fmax= 6.54244e+03, atom= 14 46, Dmax= 1.4e-02 nm, Epot= -3.71522e+04 Fmax= 9.78496e+03, atom= 14 47, Dmax= 1.7e-02 nm, Epot= -3.72173e+04 Fmax= 9.63259e+03, atom= 14 48, Dmax= 2.0e-02 nm, Epot= -3.72214e+04 Fmax= 1.36869e+04, atom= 14 49, Dmax= 2.4e-02 nm, Epot= -3.72779e+04 Fmax= 1.38147e+04, atom= 14 51, Dmax= 1.4e-02 nm, Epot= -3.74609e+04 Fmax= 2.55846e+03, atom= 14 53, Dmax= 8.6e-03 nm, Epot= -3.75364e+04 Fmax= 7.70589e+03, atom= 14 54, Dmax= 1.0e-02 nm, Epot= -3.76121e+04 Fmax= 4.80687e+03, atom= 14 55, Dmax= 1.2e-02 nm, Epot= -3.76370e+04 Fmax= 9.96253e+03, atom= 14 56, Dmax= 1.5e-02 nm, Epot= -3.77139e+04 Fmax= 7.73810e+03, atom= 14 58, Dmax= 8.9e-03 nm, Epot= -3.77915e+04 Fmax= 2.65117e+03, atom= 14 59, Dmax= 1.1e-02 nm, Epot= -3.78414e+04 Fmax= 1.03758e+04, atom= 14 60, Dmax= 1.3e-02 nm, Epot= -3.79406e+04 Fmax= 5.14878e+03, atom= 14 62, Dmax= 7.7e-03 nm, Epot= -3.79939e+04 Fmax= 3.96477e+03, atom= 14 63, Dmax= 9.3e-03 nm, Epot= -3.80329e+04 Fmax= 7.00272e+03, atom= 14 64, Dmax= 1.1e-02 nm, Epot= -3.80828e+04 Fmax= 6.20802e+03, atom= 14 65, Dmax= 1.3e-02 nm, Epot= -3.81051e+04 Fmax= 9.53587e+03, atom= 14 66, Dmax= 1.6e-02 nm, Epot= -3.81487e+04 Fmax= 9.34186e+03, atom= 14 68, Dmax= 9.6e-03 nm, Epot= -3.82403e+04 Fmax= 1.92036e+03, atom= 14

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 2000 in 69 steps Potential Energy = -3.8240305e+04 Maximum force = 1.9203647e+03 on atom 14 Norm of force = 5.7344648e+03 gcq#260: "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)