Justin A. Lemkul wrote:
ERIKSSON, EMMA wrote:
I was using those "strange" values of tau_p and compressibility to
keep the z
box length fixed in order to avoid problems associated with scaling the
positions of the molecules in the box when we constrain the distance
between
DPPC and the smal
Gromacs Users' List Ämne: Re:
[gmx-users] Constrained simulations crash when bilayer moves in the z
direction in the box
ERIKSSON, EMMA wrote:
Pcoupl = Parrinello-Rahman pcoupltype =
semiisotropic tau_p= 1.0 1.0e-14 compressibility
=
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Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in
the z direction in the box
ERIKSSON, EMMA wrote:
> Pcoupl = Parrinello-Rahman
> pcoupltype
ERIKSSON, EMMA wrote:
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p= 1.0 1.0e-14
compressibility = 4.5e-5 4.5e-15
I would bet almost anything that this is the cause of your problem. How did you
come up with these bi
alway, Ireland
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Justin A. Lemkul [jalem...@vt.edu]
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...@gromacs.org [gmx-users-
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you should remove the water and li
] för Justin A. Lemkul [jalem...@vt.edu]
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[gmx-users] Constrained simulations crash when bilayer moves in the z
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ERIKSSON, EMMA wrote:
The last section of my mdp file:
- Galway
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tional University of Ireland - Galway Galway, Ireland
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eland
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National University of Ireland - Galway
Galway, Ireland
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.
-Justin
Emma
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pbc.
Emma
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romacs.org] för XAvier Periole [x.peri...@rug.nl]
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*Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer
moves in the z direction in the box
you should remove the water and lipid bilayer COM separately. I am
ce.
Emma
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] för
Justin A. Lemkul [jalem...@vt.edu]
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ERIKSSON, EMMA wrote:
> Hi again,
> Thanks Xavier for your reply. I
XAvier
Periole [x.peri...@rug.nl]
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direction in the box
you should remove the water and lipid bilayer COM separately.
I am not sure what you should
idn't understand you explanation.
Emma
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n't understand you explanation.
Emma
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för XAvier Periole [x.peri...@rug.nl]
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Sorry that I didn't understand you explanation.
Emma
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Ämne: Re: [gmx-users] Cons
The crash seems to be expected as by crossing the pbc the distance
will change significantly
and in way the algorithm can not handle.
Note that the overall translational motion of your system should
always be removed.
The removal of the COM motion of your bilayer should be sufficient to
Hi all!
I have a problem regarding lipid bilayer simulations in Gromacs 4. During some
of my simulations the whole system is moving in the z direction in the box,
meaning that after some time the lipids are going out in the bottom of the box
and coming in in the top of the box, since I'm using
Dear Giuseppe:
This is a pretty good example of how it can be useful to completely
describe what you are doing at first posting. What you mention could
easily be a problem for a couple of reasons:
1. The manual indicates that you may need more than one shake
iteration in this case (or at
Dear Chris:
I don't think it is something related to pbc because my solutes are well
inside the simulation box (as I told you before I visualize them via a movie
while the simulation proceeds).
Nor it is something related to the barostat because I saw that warning
and in order to try to see it wo
Dear Giuseppe:
OK, those are the forces. They seem pretty huge and massively
fluctuating, although I use umbrella sampling myself so this might be
quite normal for constraint sampling (something for you to look into).
The only thing that comes to mind is that your running up against a
pbc
Got it!
Ok, first lines:
# CONSTRAINT3.0
# Component selection: 1 1 1
# nSkip 1
# Ref. Group 'protein_b'
# Nr. of pull groups 1
# Group 1 'protein_a' Pos. 3.099513 2.982803 3.377482
#
0.00-787.501479
0.002000-271.159600
0.004000-1147.35
Dear Giuseppe:
*** What I am looking for is raw -pd pull.pdo data from the first run. ***
It looks like you did not define a name for -pd:
mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c
output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 *
so based on
Chris:
you're right man, let me be more concise.
Here there is the execution line I used:
mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c
output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 *
As for the pull.ppa file, here you go:
; GENERAL
verbose
Dear Giuseppe:
I don't think your method of showing the change is very good since it
introduces unnecessary variables (e.g. did you use the correct files
for the second run).
What I am looking for is raw -pd pull.pdo data from the first run. I
found no such file in the body of the email
Hi Chris,
the pdo file was attached at the bottom of my previous e-mail. As for
the output, you may read the information about the COMs in the md.log
file. Here there is an extended portion of it at the beginning of the
simulation:
**
Please provide actual gromacs output and tell us where it is from. I
know it's sad, but not all of us can recall what the gromacs 3.3.3
.pdo file format looked like. So please include a sufficiently large
portion of the file to help us recall. If, on the other hand, these
values that you pl
Hello,
I'm trying to do constrained simulations of a system consisting of two
solvated proteins separated at a given distance. Inside the box there are
also
around 14.000 water molecules. At the bottom there is the .pdo
file (I'm using gromacs 3.3.3).
However, it seems as it does not work. At the
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