[gmx-users] increasing cut-off and PME grid spacing

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 21 06:31:57 CEST 2011

Hsin-Lin Chiang wrote:
> Hi, Justin
> Sorry for the unclear message.
> My box vector in .gro file are 44.22834  44.22834  44.22834 and the 
> number of atoms is 20171

You've set an unreasonably large box, as I expected.  The box should be set in 
nm, not Angstrom.  20171 atoms is a fairly small system, and in effect what 
you've created is a protein in a droplet of water, surrounded by vacuum.  90% of 
the work done by PME will be to calculate a grid of nothing.

> The output of grompp is shown below,
> I don't know if it is enough and I'm sorry I don't know how should I do 
> after you reply.
> Could you please give me more messages in detail?

The solution is to set a correct box, unless your objective is to simulate a 
droplet, in which case you have no choice but to take the performance loss 
inherent to using PME.


> Hsin-Lin
> -----------------------------------------------------------
>         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.
>                                 :-)  grompp  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f       test.mdp  Input        grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c  ../3eq/eq.gro  Input        Structure file: gro g96 pdb tpr etc.
>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>   -n ../initial/index.ndx  Input, Opt!  Index file
>   -p ../initial/insulin.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o       test.tpr  Output       Run input file: tpr tpb tpa
>   -t  ../3eq/eq.trr  Input, Opt!  Full precision trajectory: trr trj cpt
>   -e       ener.edr  Input, Opt.  Energy file
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    0       Set the nicelevel
> -[no]v       bool   no      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. Not for normal use and may generate
>                             unstable systems
> -[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.3#
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> turning H bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning H bonds into constraints...
> Velocities were taken from a Maxwell distribution at 300 K
> Number of degrees of freedom in T-Coupling group Protein is 1448.89
> Number of degrees of freedom in T-Coupling group non-Protein is 39297.11
> Reading Coordinates and Box size from old trajectory
> Will read whole trajectory
> Velocities generated: ignoring velocities in input trajectory
> trn version: GMX_trn_file (single precision)
> Last frame        800 time  800.000
> Using frame at t = 800 ps
> Starting time for run is 0 ps
> Largest charge group radii for Van der Waals: 0.248, 0.178 nm
> Largest charge group radii for Coulomb:       0.248, 0.214 nm
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 224x224x224, spacing 0.197 0.197 0.197
> Estimate for the relative computational load of the PME mesh part: 1.00
> NOTE 1 [file test.mdp]:
>   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
> NOTE 2 [file test.mdp]:
>   This run will generate roughly 3481 Mb of data
> There were 2 notes
> Back Off! I just backed up test.tpr to ./#test.tpr.3#
> gcq#159: "Way to Go Dude" (Beavis and Butthead)


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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