[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken
Tsjerk Wassenaar
tsjerkw at gmail.com
Mon Jan 11 20:26:24 CET 2010
Now try hard to resist running on multiple processors...
Tsjerk
On Mon, Jan 11, 2010 at 8:11 PM, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
>
>
>
> Today's Topics:
>
> 1. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken
> (Chih-Ying Lin)
> 2. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output
> file) (Chih-Ying Lin)
>
>
> ------------------------------
> ----------------------------------------
>
> Message: 1
> Date: Sun, 10 Jan 2010 10:11:17 +0800
> From: Chih-Ying Lin <chihying2008 at gmail.com>
> Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation
> Broken
> To: gmx-users at gromacs.org
> Message-ID:
> <5777f3841001091811l41fbe079ida9822609fc8e260 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi
> 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the
> simulation on Gromacs.
> System = 6LYZ.pdb + CL- + water molecules
>
> Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all.
> Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step
> Position restrained MD.
>
> The commands are as follows.
> minim.mdp and pr.mdp are as follows.
> And outputs are as follows.
>
> Any thing wrong?
> Thank you
> Lin
>
>
> 1. Energy minimization of the structure (vacuum)
> pbc=no
> grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr
> mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-vacuum
>
>
> 2. Periodic boundary conditions
> editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -box 6.0 6.0
> 6.0
>
>
> 3. Solvent addition
> genbox_mpi -cp 6LYZ-PBC.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro
>
>
> 4. Addition of ions: counter charge and concentration
> grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr
> genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 8 -nname CL-
>
>
> 5 Energy minimization of the solvated system => Potential Energy went to
> the very negative number
> pbc =xyz (minim.mdp)
> grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
> 6LYZ-EM-solvated
> mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-solvated
>
>
> 6 Relaxation of solvent and hydrogen atom positions: Position restrained
> MD => Simulation Broke
> grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr
> mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR
>
>
> =====================================================================================================
> minim.mdp
>
> ; LINES STARTING WITH ';' ARE COMMENTS
> title = Minimization of Lysozyme (1LW9.pdb) ; Title of run
> ; The following lines tell the program the standard locations where to
> find certain files
> cpp = /lib/cpp ; Preprocessor
> ; Definea can be used to control processes
> define = -DFLEXIBLE
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol = 1.0 ; Stop minimization when the maximum force <
> 1.0 kJ/mol
> nsteps = 50000 ; Maximum number of (minimization) steps
> to perform
> nstenergy = 1 ; Write energies to disk every nstenergy
> steps
> energygrps = System ; Which energy group(s) to write to disk
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 5 ; Frequency to update the neighbor list
> and long range forces
> ns_type = simple ; Method to determine neighbor list
> (simple, grid)
> rlist = 1.0 ; Cut-off for making neighbor list (short
> range forces)
> coulombtype = cut-off ; Treatment of long range electrostatic
> interactions
> rcoulomb = 1.0 ; long range electrostatic cut-off
> rvdw = 1.0 ; long range Van der Waals cut-off
> constraints = none ; Bond types to replace by constraints
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>
> =================================================================================================
> pr.mdp
>
> ; VARIOUS PREPROCESSING OPTIONS
> title =
> cpp = /lib/cpp
> include =
> define = -DPOSRES
> ; RUN CONTROL PARAMETERS
> integrator = md
> tinit = 0
> dt = 0.001
> nsteps = 5000
> nstcomm = 0
> ; OUTPUT CONTROL OPTIONS
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 10
> nstenergy = 1
> nstxtcout = 0
> xtc_precision = 1000
> xtc-grps = System
> energygrps = Protein Non-Protein
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist = 5
> ns-type = Grid
> pbc = xyz
> rlist = 0.9
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype = Reaction-Field
> rcoulomb = 1.4
> epsilon_rf = 78
> epsilon_r = 1
> vdw-type = Cut-off
> rvdw = 1.4
> ; Temperature coupling
> Tcoupl = Berendsen
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 200 200
> ; Pressure coupling
> Pcoupl = No
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = yes
> gen_temp = 200.0
> gen_seed = 1735
> ; OPTIONS FOR BONDS
> constraints = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start = no
> lincs-order = 4
> lincs-iter = 1
> lincs-warnangle = 30
>
>
>
>
>
>
> =======================================================================================================
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> ------------------------------
>
> Message: 2
> Date: Sun, 10 Jan 2010 10:29:35 +0800
> From: Chih-Ying Lin <chihying2008 at gmail.com>
> Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation
> Broken (output file)
> To: gmx-users at gromacs.org
> Message-ID:
> <5777f3841001091829r4e88d83fs8eb680bb99077aa6 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi
> 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the
> simulation on Gromacs.
> System = 6LYZ.pdb + CL- + water molecules
>
> Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all.
> Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step
> Position restrained MD.
>
> The commands are as follows.
> minim.mdp and pr.mdp are as follows.
> And outputs are as follows.
>
> Any thing wrong?
> Thank you
> Lin
>
>
> =======================================================================================================
>
> - Hide quoted text -
> grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
> 6LYZ-EM-solvated
> :-) G R O M A C S (-:
> Good gRace! Old Maple Actually Chews Slate
> :-) VERSION 4.0.5 (-:
> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2008, 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_mpi (-:
> Option Filename Type Description
> ------------------------------------------------------------
> -f minim.mdp Input, Opt! grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c 6LYZ-solvated.gro Input Structure file: gro g96 pdb tpr tpb tpa
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -n index.ndx Input, Opt. Index file
> -p 6LYZ.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o 6LYZ-EM-solvated.tpr Output Run input file: tpr tpb tpa
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> -e ener.edr Input, Opt. Energy file: edr ene
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -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.
> -[no]rmvsbds bool yes Remove constant bonded interactions with virtual
> sites
> -maxwarn int 0 Number of allowed warnings during input
> processing
> -[no]zero bool no Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum bool yes Renumber atomtypes and minimize number of
> atomtypes
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2nb.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2bon.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp
> Generated 380 of the 1326 non-bonded parameter combinations
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'CL-'
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat
> There are: 6512 OTHER residues
> There are: 129 PROTEIN residues
> There are: 0 DNA residues
> Analysing Protein...
> Analysing Other...
> Making dummy/rest group for T-Coupling containing 20841 elements
> Making dummy/rest group for Acceleration containing 20841 elements
> Making dummy/rest group for Freeze containing 20841 elements
> Making dummy/rest group for VCM containing 20841 elements
> Number of degrees of freedom in T-Coupling group rest is 62520.00
> Making dummy/rest group for User1 containing 20841 elements
> Making dummy/rest group for User2 containing 20841 elements
> Making dummy/rest group for XTC containing 20841 elements
> Making dummy/rest group for Or. Res. Fit containing 20841 elements
> Making dummy/rest group for QMMM containing 20841 elements
> T-Coupling has 1 element(s): rest
> Energy Mon. has 1 element(s): System
> 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...
> NOTE 1 [file minim.mdp, line unknown]:
> You are using a plain Coulomb cut-off, which might produce artifacts.
> You might want to consider using PME electrostatics.
> This run will generate roughly 242 Mb of data
> writing run input file...
> There was 1 note
> Back Off! I just backed up 6LYZ-EM-solvated.tpr to
> ./#6LYZ-EM-solvated.tpr.1#
> gcq#13: "If Life Seems Jolly Rotten, There's Something You've Forgotten !"
> (Monty Python)
>
>
>
> =================================================================================================================
>
> grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr
> :-) G R O M A C S (-:
> Giant Rising Ordinary Mutants for A Clerical Setup
> :-) VERSION 4.0.5 (-:
> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2008, 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_mpi (-:
> Option Filename Type Description
> ------------------------------------------------------------
> -f pr.mdp Input, Opt! grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c 6LYZ-EM-solvated.gro Input Structure file: gro g96 pdb tpr tpb
> tpa
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -n index.ndx Input, Opt. Index file
> -p 6LYZ.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o 6LYZ-PR.tpr Output Run input file: tpr tpb tpa
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> -e ener.edr Input, Opt. Energy file: edr ene
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -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.
> -[no]rmvsbds bool yes Remove constant bonded interactions with virtual
> sites
> -maxwarn int 0 Number of allowed warnings during input
> processing
> -[no]zero bool no Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum bool yes Renumber atomtypes and minimize number of
> atomtypes
> Ignoring obsolete mdp entry 'cpp'
> Replacing old mdp entry 'unconstrained-start' by 'continuation'
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> checking input for internal consistency...
> NOTE 1 [file pr.mdp, line unknown]:
> The Berendsen thermostat does not generate the correct kinetic energy
> distribution. You might want to consider using the V-rescale thermostat.
> processing topology...
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2nb.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2bon.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp
> Generated 380 of the 1326 non-bonded parameter combinations
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL-'
> turning all bonds into constraints...
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 200 K
> Reading position restraint coords from 6LYZ-EM-solvated.gro
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat
> There are: 6512 OTHER residues
> There are: 129 PROTEIN residues
> There are: 0 DNA residues
> Analysing Protein...
> Analysing Other...
> Making dummy/rest group for Acceleration containing 20841 elements
> Making dummy/rest group for Freeze containing 20841 elements
> Making dummy/rest group for VCM containing 20841 elements
> Number of degrees of freedom in T-Coupling group Protein is 2618.00
> Number of degrees of freedom in T-Coupling group Non-Protein is 39048.00
> Making dummy/rest group for User1 containing 20841 elements
> Making dummy/rest group for User2 containing 20841 elements
> Making dummy/rest group for Or. Res. Fit containing 20841 elements
> Making dummy/rest group for QMMM containing 20841 elements
> T-Coupling has 2 element(s): Protein Non-Protein
> Energy Mon. has 2 element(s): Protein Non-Protein
> 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): System
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
> This run will generate roughly 3 Mb of data
> writing run input file...
> There was 1 note
> Back Off! I just backed up 6LYZ-PR.tpr to ./#6LYZ-PR.tpr.1#
> gcq#52: "I'm a Wishbone and I'm Breaking" (Pixies)
>
>
>
> ====================================================================================================
>
>
>
> ======================================================================================================
> .out file
>
>
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 1005 1006 41.4 0.1625 0.1078 0.1430
> 1006 1007 30.6 0.1044 0.0899 0.1000
> 1077 1081 129.5 0.2893 0.5930 0.1390
> 1077 1078 102.3 0.0542 1.1847 0.1090
> 1073 1077 167.5 1.0876 0.9651 0.1390
> 1073 1076 57.2 0.6969 1.7573 0.1390
> 1074 1076 63.8 0.6555 1.2119 0.1330
> 1074 1075 101.0 1.3130 1.1709 0.1000
> 1071 1074 108.5 1.0586 0.4070 0.1330
> 1071 1072 94.2 0.6662 1.3755 0.1090
> 1070 1071 114.1 0.6490 0.6753 0.1330
> 1070 1073 155.5 1.0880 1.0783 0.1390
> 1069 1070 78.1 0.2488 1.2798 0.1530
>
>
>
>
>
> --
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--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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