I'm getting control over my .mdp files, cutting down on the generation of
data for which I currently have no use. I just changed the nstenergy
parameter to 2500 cycles, much larger than its default value of 100 cycles.
This reduced logging still gives me plenty of data for monitoring the
Erik Marklund wrote
On 11 okt 2012, at 16.17, R.Vidya Rajendran (10PHD013) wrote:
Hello Friends,
I have two very specific queries regarding gromacs output files.
1) Since we can generate .xtc file during mdrun, Is is possible to
stop generating .trr files, because it used to be very
Update:
Ladasky wrote
Justin Lemkul wrote
Random segmentation faults are really hard to debug. Can you resume the
run
using a checkpoint file? That would suggest maybe an MPI problem or
something
else external to Gromacs. Without a reproducible system and a debugging
backtrace
Justin Lemkul wrote
My first guess would be a buggy MPI implementation. I can't comment on
hardware
specs, but usually the random failures seen in mdrun_mpi are a result of
some
generic MPI failure. What MPI are you using?
I am using the OpenMPI package, version 1.4.3. It's one of three
Justin Lemkul wrote
Random segmentation faults are really hard to debug. Can you resume the
run
using a checkpoint file? That would suggest maybe an MPI problem or
something
else external to Gromacs. Without a reproducible system and a debugging
backtrace, it's going to be hard to
Bumping this once before the weekend, hoping to get some help.
I am getting segmentation fault errors at 1 to 2 million cycles into my
production MD runs, using GROMACS 4.5.4. If these errors are a consequence
of a poorly-equilibrated system, I am no longer getting the right kind of
error
So I have spent the past few weeks debugging my equilibration protocols,
which were an odd hybrid of examples ranging from GROMACS 3.3 up to GROMACS
4.5. I have cleaned out old code. I added an in vacuo energy minimization
step for the protein without solvent, and a missing NVT step after
Justin Lemkul wrote
Note that you can always select by name rather than number, i.e.:
echo Temperature | g_energy -f ener.edr
That's undocumented, as of the GROMACS 4.5.4 manual, but VERY useful.
Thanks.
--
View this message in context:
I have been trying to automate my simulation setup and monitoring. I wrote a
script which calls g_energy, and automatically generates plots of potential
energy from my EM step, temperature from my NVT equilibration step, and
pressure and density from my NPT equilibration step. For each of these
Hello again everyone,
I'm currently running GROMACS 4.5.4 on Ubuntu Linux 11.10. I'm trying to
clean up my simulation conditions. Many of my MDP files are hold-overs from
earlier versions of GROMACS, as far back as v. 3.3. I have written some
shell scripts which should handle this work
Peter C. Lai wrote
Generally it's probably not a good idea to rely on tutorials designed
around 3.3 when a google search for gromacs tutorial shows a series of
4.5.x
tutorials written by Justin himself, with explanations of why certain
steps
are conducted. (also when certain features may
Justin Lemkul wrote
So the initial equilibration was NPT?
Yes.
Justin Lemkul wrote
Did you ever try simply running NVT with
either Berendsen or V-rescale before applying any type of pressure
coupling?
No, I haven't, and I don't remember seeing that described in any work flow.
Justin
Hi Peter,
Thanks for your response.
Rather than dragging this thread too far off-topic, I'll direct you back to
my thread, where I have just posted additional details. I took a warning
message from GROMACS a bit too literally and it caused me to use conditions
that blew up my simulations.
I am
Dear Sara,
I just had a problem with my simulations that I traced to the use of the
V-rescale temperature algorithm. Here is my recent post:
http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121
V-rescale may be appropriate in
Thank you, Luca, for the link to the Ponder and Case review article.
http://maxwell.uncc.edu/abaumket/phys6203_files/Reading/force-fields.pdf
It is indeed the kind of article I have been seeking.
maybe one of the best thing to do is to test the FF vs experimental data
and check which one
I have read a variation on this advice many. many times here:
The ultimate choice of force field should be based on your reading and
understanding of their derivation and known applications/limitations, all of
which comes from the literature. Choose the one that you think is most
sound :)
I am
Hello Mark,
Thanks for your reply. It has taken me several days to make some progress
on my issues. I'm just going to address one specific point in this post.
Mark Abraham wrote
On 19/07/2012 6:52 PM, Ladasky wrote:
I once used the -deuterate option in pdb2gmx, and I am presently trying
Tsjerk Wassenaar wrote
Hi John,
Check where the unsettling water molecule is placed. If it's in the
protein. that may be the cause of the problem. Otherwise, it's some of
the other stuff you're doing, but rule out the simple things first.
Thank you Tsjerk.
I posted a reply several
Date: Wed, 11 Jul 2012 10:32:35 +0200
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx-users] Re: Water molecules cannot be settled, why?
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
cabze1sj37c49x22yfpvfqniyqjfxjcgww5dycu0k9kzucei...@mail.gmail.com
Hello, everyone,
I am reviving a discussion I started about a month back.
http://gromacs.5086.n6.nabble.com/Water-molecules-cannot-be-settled-why-tt4998059.html
I thought that I would try to work around the problem by only proceeding
with those simulations that didn't crash, but I've
Recently I have started to get crash messages in my molecular dynamics
runs which look like this:
Reading file exp37b-prep.tpr, VERSION 4.5.4 (single precision)
Making 1D domain decomposition 5 x 1 x 1
starting mdrun 'Protein in water'
50 steps, 1000.0 ps.
step 81240: Water molecule
I am starting to write my own turnkey scripts to automate GROMACS (v
4.5.4) work flow. Many of the GROMACS commands, such as pdb2gmx and
genion, have interactive options by default, meaning that you manually
enter information when the program runs.
In the tutorials, we are taught to invoke
I am trying to import PDB file snapshots from a GROMACS 4.5.4-generated
trajectory into other software tools -- specifically, Biopython. I
generate the snapshots using trjconv in GROMACS.
I am interested in the water molecules from my solvent box, so I do not
discard them. When trjconv
Following up to myself:
Looking back through the archives, I have learned that the issue of
solvent atoms being exported from trjconv into PDB files as ATOM
rather than as HETATM is an issue that was raised fully six years ago.
http://www.mail-archive.com/gmx-users@gromacs.org/msg00405.html
Hello everyone,
I've used the rot+trans option in GROMACS trjconv to superimpose groups of
atoms within a single molecular dynamics simulation. I am now interested in
modeling a protein, and a rather thoroughly scrambled circular permutation of
that same protein. I want to construct a
!
John Ladasky
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