darre...@ece.ubc.ca wrote:
Hi Mark,
I used editconf on my .gro file with zero space between my solvent and
the box and the resulting box had the exact same dimension as the
initial box. I also performed a number of simulation runs with different
If you're using editconf to define zero space, what's the point? I only ask
because it is a potential source of error if you think you're adding zero space,
but something else might be going on. Maybe you can post your editconf command
line.
What are your box dimensions? Are cut-off lengths of 2.0 and 5.0 nm appropriate
for your system? How did you determine that these cut-off's should be used?
mdp parameters hoping this would provide me some indication of the cause
of the fault but to no avail. I looked through the log files, error
files, and output files and could not find any output to help me
identify the source of my error.
It is very odd that Gromacs isn't report anything at all. No LINCS warnings?
No neighborlist errors? These would be in the .log file.
Could you please let me know how I can look at my structure at each point
as you indicate below as I do not see any files output that provide me
to do so? I tried to look at the .trr file but when I try to load it
into VMD, it causes an error. I am assuming this error is caused because
the .trr file did not complete correctly due to the segmentation fault.
Please advise.
How early is the segmentation fault occurring? I have found it useful sometimes
to set nstxout (or nstxtcout) = 1 to try to catch the first few frames if the
explosion is occurring early. In any case, gmxcheck will help determine how
many frames are present, as well as the integrity of the file (broken frames, etc).
-Justin
Thanks.
Darrell
Date: Tue, 07 Jul 2009 09:19:42 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a52868e.6010...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
darre...@ece.ubc.ca wrote:
Hi Mark,
I added the energy group exclusions as indicated in your previous
response but am still experiencing the same problem. I looked at the
.log files and see that in one log file it tells me that my box is
exploding. However, I do not have many molecules in my simulation and
therefore do not think that it is possible that my box is exploding from
pressure.
Sure, but if there's something malformed with your model physics or
starting configuration, then large forces can make anything explode.
Look at your structures at each point and see where things start to go
wrong. Make sure you've used editconf on your starting structure to
provide the right box dimensions.
Mark
Maybe if I re-state my simulation it will help you in providing me
direction on what might be causing the problem. My simulation consists
of a graphene lattice with a layer of ammonia molecules above it. The
box is very large and there is lots of empty space in the box. So I am a
little confused as to how the box could be exploding.
Thanks again in advance for your help.
Darrell Koskinen
Date: Fri, 03 Jul 2009 11:41:45 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a4d61d9.6080...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
darre...@ece.ubc.ca wrote:
Dear GROMACS Gurus,
I am experiencing a segmentation fault when mdrun executes. My simulation
has a graphene lattice with an array (layer) of ammonia molecules above
it. The box is three times the width of the graphene lattice, three
times the length of the graphene lattice, and three times the height
between the graphene lattice and the ammonia molecules. I am including
the mdp file and the error message.
Probably your system is exploding when integration fails with excessive
forces. You should look at the bottom of stdout, stderr, *and* the .log
file to diagnose. The error message you give below is merely the
diagnostic trace from the MPI library, and it not useful for finding out
what GROMACS thinks the problem might be. Further advice below.
***************************************************************************
.mdp file
title =FWS
;warnings =10
cpp =cpp
;define =-DPOSRES
;constraints =all-bonds
integrator =md
dt =0.002 ; ps
nsteps =100000
nstcomm =1000
nstxout =1000
;nstvout =1000
nstfout =0
nstlog =1000
nstenergy =1000
nstlist =1000
ns_type =grid
rlist =2.0
coulombtype =PME
rcoulomb =2.0
vdwtype =cut-off
rvdw =5.0
fourierspacing =0.12
fourier_nx =0
fourier_ny =0
fourier_nz =0
pme_order =4
ewald_rtol =1e-5
optimize_fft =yes
; This section added in to freeze hydrogen atoms at edge of graphene
lattice to prevent movement of lattice
;energygrp_excl = Edge Edge Edge Grph Grph Grph
freezegrps = Edge Grph ; Hydrogen atoms in graphene lattice are
associated with the residue Edge
See comments in 7.3.24 of manual. You need the energy group exclusions.
Mark
freezedim = Y Y Y Y Y Y; Freeze hydrogen atoms in all directions
;Tcoupl =berendsen
;tau_t =0.1 0.1
;tc-grps =protein non-protein
;ref_t = 300 300
;Pcoupl = parrinello-rahman
;tau_p = 0.5
;compressibility = 4.5e-5
;ref_p = 1.0
;gen_vel = yes
;gen_temp = 300.0
;gen_seed = 173529
***************************************************************************
***************************************************************************
ERROR IN OUTPUT FILE
[node16:25758] *** Process received signal ***
[node16:25758] Signal: Segmentation fault (11)
[node16:25758] Signal code: Address not mapped (1)
[node16:25758] Failing at address: 0xfffffffe1233e230
[node16:25758] [ 0] /lib64/libpthread.so.0 [0x3834a0de80]
[node16:25758] [ 1] /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6)
[0x2ba295dd0606]
[node16:25758] [ 2] /usr/lib64/libmd_mpi.so.4(do_pme+0x808)
[0x2ba295dd4058]
[node16:25758] [ 3] /usr/lib64/libmd_mpi.so.4(force+0x8de)
[0x2ba295dba5be]
[node16:25758] [ 4] /usr/lib64/libmd_mpi.so.4(do_force+0x5ef)
[0x2ba295ddeaff]
[node16:25758] [ 5] mdrun_mpi(do_md+0xe23) [0x411193]
[node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40) [0x4142f0]
[node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9]
[node16:25758] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x3833e1d8b4]
[node16:25758] [ 9] mdrun_mpi [0x40429a]
[node16:25758] *** End of error message ***
mpirun noticed that job rank 7 with PID 25758 on node node16 exited on
signal 11 (Segmentation fault).
7 processes killed (possibly by Open MPI)
***************************************************************************
Could you please let me know what you think may be causing the fault?
Much thanks in advance.
Darrell Koskinen
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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