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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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