[gmx-users] genconf and bonded interactions

Fabio Affinito f.affinito at cineca.it
Wed Jul 27 16:41:52 CEST 2011


On 07/27/2011 04:12 PM, Justin A. Lemkul wrote:
>
>
> Fabio Affinito wrote:
>> On 07/27/2011 03:54 PM, Justin A. Lemkul wrote:
>>>
>>>
>>> Fabio Affinito wrote:
>>>> This is the mdrun output:
>>>>
>>>> Initializing Domain Decomposition on 4096 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: 30.031 nm, LJ-14, atoms 40702 40705
>>>> multi-body bonded interactions: 30.031 nm, Angle, atoms 40701 40704
>>>> Minimum cell size due to bonded interactions: 33.035 nm
>>>> Maximum distance for 7 constraints, at 120 deg. angles, all-trans:
>>>> 1.139 nm
>>>> Estimated maximum distance required for P-LINCS: 1.139 nm
>>>> Guess for relative PME load: 0.43
>>>> Will use 2400 particle-particle and 1696 PME only nodes
>>>> This is a guess, check the performance at the end of the log file
>>>> Using 1696 separate PME nodes
>>>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>>>> Optimizing the DD grid for 2400 cells with a minimum initial size of
>>>> 41.293 nm
>>>> The maximum allowed number of cells is: X 0 Y 0 Z 0
>>>>
>>>> -------------------------------------------------------
>>>> Program mdrun_mpi_bg, VERSION 4.5.4
>>>> Source code file: domdec.c, line: 6438
>>>>
>>>> Fatal error:
>>>> There is no domain decomposition for 2400 nodes that is compatible
>>>> with the given box and a minimum cell size of 41.2932 nm
>>>> Change the number of nodes or mdrun option -rdd or -dds
>>>> Look in the log file for details on the domain decomposition
>>>> For more information and tips for troubleshooting, please check the
>>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>> -------------------------------------------------------
>>>>
>>>
>>> This is bizarre. Did you fix the periodicity of the original coordinate
>>> file (conf_start.gro) and rebuild the system, or did you try to run
>>> trjconv on the replicated system? The former is the correct approach.
>>>
>>> -Justin
>>>
>> This is what I did (in the chronological order):
>>
>> 1) trjconv -f conf_start.gro -o conf_whole.gro -pbc whole
>
> Presumably in conjunction with a .tpr file, in order for this to work?

Ok, I added.

>
>> 2) genconf -f conf_whole.gro -o out.gro -nbox 2 2 1
>> 3) i modified the topol.top (modifying the number of molecules)
>> 4) grompp -f grompp.mdp -c out.gro -p topol.top -maxwarn 3
>
> What are the warnings you are trying to circumvent? Please provide the
> full grompp output. I can think of a few other possibilities for the
> source of your problem, but I do not want to venture idle guesswork
> without seeing all of the warnings you've got.

This is the full grompp output:

>                          :-)  G  R  O  M  A  C  S  (-:
>
>                Gromacs Runs One Microsecond At Cannonball Speeds
>
>                             :-)  VERSION 4.0.7  (-:
>
>
>       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  (-:
>
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f     grompp.mdp  Input, Opt!  grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c        out.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      topol.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o      topol.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    3       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 'dihre-tau'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Generated 354061 of the 354061 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 354061 of the 354061 1-4 parameter combinations
> Opening library file /bgsys/local/gromacs/4.0.7/share/gromacs/top/spc.itp
> Opening library file /bgsys/local/gromacs/4.0.7/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_B'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_C'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_D'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'POPC'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'POPG'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'K+'
> turning all bonds into constraints...
>
> NOTE 1 [file topol.top, line 50]:
>   System has non-zero total charge: 1.217723e-04
>
>
>
> processing coordinates...
> Warning: atom name 18113 in topol.top and out.gro does not match (MN1 - CN1)
> Warning: atom name 18114 in topol.top and out.gro does not match (MN2 - CN2)
> Warning: atom name 18115 in topol.top and out.gro does not match (N - CN3)
> Warning: atom name 18116 in topol.top and out.gro does not match (H1 - N)
> Warning: atom name 18117 in topol.top and out.gro does not match (H2 - CA)
> Warning: atom name 18118 in topol.top and out.gro does not match (H3 - CB)
> Warning: atom name 18119 in topol.top and out.gro does not match (CA - OA)
> Warning: atom name 18120 in topol.top and out.gro does not match (HA - P)
> Warning: atom name 18121 in topol.top and out.gro does not match (MCB1 - OB)
> Warning: atom name 18122 in topol.top and out.gro does not match (MCB2 - OC)
> Warning: atom name 18123 in topol.top and out.gro does not match (CB - OD)
> Warning: atom name 18124 in topol.top and out.gro does not match (HB1 - CC)
> Warning: atom name 18125 in topol.top and out.gro does not match (HB2 - CD)
> Warning: atom name 18126 in topol.top and out.gro does not match (HB3 - OE)
> Warning: atom name 18127 in topol.top and out.gro does not match (C - C1A)
> Warning: atom name 18128 in topol.top and out.gro does not match (O - O1A)
> Warning: atom name 18129 in topol.top and out.gro does not match (N - C1B)
> Warning: atom name 18130 in topol.top and out.gro does not match (H - C1C)
> Warning: atom name 18131 in topol.top and out.gro does not match (CA - C1D)
> Warning: atom name 18132 in topol.top and out.gro does not match (HA - C1E)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file topol.top, line 50]:
>   219116 non-matching atom names
>   atom names from topol.top will be used
>   atom names from out.gro will be ignored
>
>
> double-checking input for internal consistency...
> Calculating parameters for virtual sites
> Calculating parameters for virtual sites
> Calculating parameters for virtual sites
> Calculating parameters for virtual sites
> Cleaning up constraints and constant bonded interactions with virtual sites
> Removed   1305           Angles with virtual sites,  6251 left
> Removed    480     Proper Dih.s with virtual sites,   363 left
> Converted 2230      Constraints with virtual sites to connections,  2596 left
> Warning: removed 582 Constraints with vsite with Virtual site 3out construction
>          This vsite construction does not guarantee constant bond-length
>          If the constructions were generated by pdb2gmx ignore this warning
> Cleaning up constraints and constant bonded interactions with virtual sites
> Removed   1305           Angles with virtual sites,  6251 left
> Removed    480     Proper Dih.s with virtual sites,   363 left
> Converted 2230      Constraints with virtual sites to connections,  2596 left
> Warning: removed 582 Constraints with vsite with Virtual site 3out construction
>          This vsite construction does not guarantee constant bond-length
>          If the constructions were generated by pdb2gmx ignore this warning
> Cleaning up constraints and constant bonded interactions with virtual sites
> Removed   1305           Angles with virtual sites,  6251 left
> Removed    480     Proper Dih.s with virtual sites,   363 left
> Converted 2230      Constraints with virtual sites to connections,  2596 left
> Warning: removed 582 Constraints with vsite with Virtual site 3out construction
>          This vsite construction does not guarantee constant bond-length
>          If the constructions were generated by pdb2gmx ignore this warning
> Cleaning up constraints and constant bonded interactions with virtual sites
> Removed   1305           Angles with virtual sites,  6251 left
> Removed    480     Proper Dih.s with virtual sites,   363 left
> Converted 2230      Constraints with virtual sites to connections,  2596 left
> Warning: removed 582 Constraints with vsite with Virtual site 3out construction
>          This vsite construction does not guarantee constant bond-length
>          If the constructions were generated by pdb2gmx ignore this warning
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file /bgsys/local/gromacs/4.0.7/share/gromacs/top/aminoacids.dat
> There are: 110272      OTHER residues
> There are:  4160    PROTEIN residues
> There are:     0        DNA residues
> Analysing Protein...
> Analysing Other...
> Making dummy/rest group for Acceleration containing 485796 elements
> Making dummy/rest group for Freeze containing 485796 elements
> Making dummy/rest group for Energy Mon. containing 485796 elements
> Number of degrees of freedom in T-Coupling group System is 896777.00
> Making dummy/rest group for User1 containing 485796 elements
> Making dummy/rest group for User2 containing 485796 elements
> Making dummy/rest group for XTC containing 485796 elements
> Making dummy/rest group for Or. Res. Fit containing 485796 elements
> Making dummy/rest group for QMMM containing 485796 elements
> T-Coupling       has 1 element(s): System
> 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): System
> 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...
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 294x294x98, spacing 0.089 0.089 0.089
> Estimate for the relative computational load of the PME mesh part: 0.54
>
> NOTE 2 [file aminoacids.dat, line 1]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing
>
> This run will generate roughly 37 Mb of data
> writing run input file...
>
> There were 2 notes
>
> There was 1 warning
>
> Back Off! I just backed up topol.tpr to ./#topol.tpr.1#
>
> gcq#148: "Everybody's Good Enough For Some Change" (LIVE)
>



-- 
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198



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