darre...@ece.ubc.ca wrote:
Hi Justin,
Thanks for the explanation of the difference between EM & equilibration.
Since in my model, I: (i) only have the graphene sheet and ammonia
molecules spaced reasonably far apart from each other (1332 NH3
molecules in a 38x38x38 box) and from the graphene sheet (distance
between the closest ammonia molecule and the graphene sheet is greater
than the molecular diameter of ammonia - maybe this is too close and
could be causing my problem?); (ii) freeze the graphene sheet; I am
thinking equilibration is not required in my model. Please let me know
if you think I still need to perform equilibration.
Yes, the EM did converge satisfactorily. Here is the output from EM:
Steepest Descents converged to Fmax < 250 in 61 steps
Potential Energy = 4.6094102e+04
Maximum force = 2.4543298e+02 on atom 1
Norm of force = 7.5803179e+03
Is this a reasonable value for FMax?
Your Fmax looks fine. Why is it necessary to freeze the graphene sheet? Why
not use position restraints (to rule out funky behavior of being frozen)?
Did you ever obtain a trajectory with enough frames that you could watch? What
happened?
-Justin
Thanks again for your help.
Darrell
Date: Thu, 16 Jul 2009 07:15:12 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a5f0bc0.4020...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
darre...@ece.ubc.ca wrote:
Hi Mark,
I do not do any equilibration, I only do energy minimization as in the
"GROMACS Tutorial for Solvation Study of Spider Toxin Peptide". Please
let me know if I need to do equilibration and what is the difference
between energy minimization and equilibration as this is not clear to me.
Did the EM converge satisfactorily? What was Fmax?
Unlike EM, equilibration is an MD process; for a protein system, one generally
position-restrains the protein and allows the surrounding solvent to optimize
around the structure.
-Justin
Here is an mdp file for a run that actually completed successfully:
title =Graphene
;warnings =10
cpp =cpp
;define =-DPOSRES
constraints =none
integrator =md
dt =0.002 ; ps
nsteps =10000
nstcomm =100
nstxout =100
;nstvout =1000
nstfout =0
nstlog =100
nstenergy =100
nstlist =100
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 freezes graphene lattice
energygrps = Grph NH3
energygrp_excl = Grph Grph
freezegrps = Grph ; Freeze graphene lattice
freezedim = Y Y Y; in all directions
Tcoupl =berendsen
tau_t =0.5 0.5
tc-grps =NH3 Grph
ref_t =300 300
;coupl = parrinello-rahman
;tau_p = 1.5
;compressibility = 1.3
;ref_p = 0.061
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
And here is a copy of an mdp file for a run that did not complete
successfully:
title =Graphene
;warnings =10
cpp =cpp
;define =-DPOSRES
constraints =none
integrator =md
dt =0.002 ; ps
nsteps =30000
nstcomm =500
nstxout =500
;nstvout =1000
nstfout =0
nstlog =500
nstenergy =500
nstlist =500
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 freezes graphene lattice
energygrps = Grph NH3
energygrp_excl = Grph Grph
freezegrps = Grph ; Freeze graphene lattice
freezedim = Y Y Y; in all directions
Tcoupl =berendsen
tau_t =0.5 0.5
tc-grps =NH3 Grph
ref_t =300 300
;coupl = parrinello-rahman
;tau_p = 1.5
;compressibility = 1.3
;ref_p = 0.061
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Please let me know what you think might be the problem.
Thanks
Darrell
Date: Thu, 16 Jul 2009 09:47:49 +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: <4a5e6aa5.4040...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
darre...@ece.ubc.ca wrote:
Hi Mark,
Yes, I know that the box dimensions are defined in the last line of the
.gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm
in the .gro file.
OK.
I looked through my .gro file to ensure none of the atoms had coordinates
outside the 38x38x38 box. While I was reviewing the file I did notice
that some coordinates had negative values, slightly negative, but
negative none the less. Could this be causing the segmentation fault
between time step 10,000 and time step 30,000? Why wouldn't the
negative coordinates cause a segmentation fault much earlier?
The absolute value of the coordinates is irrelevant.
Your choice of 2.0 for rcoulomb is likely suboptimal for PME. Some
smaller value is probably more efficient, but this will not be the cause
of your problem.
What is your system preparation regime? (i.e. EM + equilibration)
Can you post a corrected and current .mdp file?
Mark
Date: Wed, 15 Jul 2009 16:59:21 +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: <4a5d7e49.9020...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
darre...@ece.ubc.ca wrote:
Hi Justin,
I was experiencing the problem before someone suggested using editconf so
I do not think the problem is being caused by editconf. But anyway here
is my editconf command. Let me know if you a source of error in this
command line.
editconf -f graphene.gro -n index.ndx -o graphene_ec.gro
I did not want to add in additional space between the solvent and the box
as I saw no reason for doing so. And hence that is why I originally did
not use editconf.
My box dimensions are 38nm x 38nm x 38nm.
The box dimensions are defined in the bottom line of the .gro file, and
not by the positions of the atoms in that file. If you haven't ever set
them to be suitable for your coordinates with editconf, then they might
not be.
Mark
I used cutoffs of 2 nm & 5 nm
for my system so ensure the cutoff occured at a distance where the
potentials were stabalized (not changing). I guess I could use shorter
cutoffs such as 1.5 nm & 2 nm and this may decrease my computation time.
I also thought that I needed to use larger cut-offs since I am dealing
in the gas phase and there is greater ditance between the atoms in my
simulation than in liquid-based simulations.
In the .log files, I do not see any LINCS warnings or neighborlist
errors.
I ran gmxcheck on a .trr file and was presented with the following
output:
*********************************************
Checking file mdtraj.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
# Atoms 10482
Last frame 5 time 1.000
Item #frames Timestep (ps)
Step 6 0.2
Time 6 0.2
Lambda 6 0.2
Coords 6 0.2
Velocities 6 0.2
Forces 0
Box 6 0.2
*********************************************
I ran two additional simulations with different values for nsteps and
nstxxxx paramaters and have the following to report:
When I run a simulation with the following parameters it completes
successfully and I see, in the log file, the system output every 100
time steps.
nsteps =10000
nstcomm =100
nstxout =100
nstfout =0
nstlog =100
nstenergy =100
nstlist =100
When I run a simulation with the following parameters it fails with a
sementation fault and, in the log file, I do not see system output every
500 time steps.
nsteps =30000
nstcomm =500
nstxout =500
nstfout =0
nstlog =500
nstenergy =500
nstlist =500
Please let me know what you think might be the problem.
Thank you very much.
Darrell
Date: Mon, 13 Jul 2009 15:37:15 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a5b8ceb.4020...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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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========================================
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Department of Biochemistry
Virginia Tech
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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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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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