Hello Yang,
It was asked twice if you ran serial or parallel and I did not see an
answer to that question.
we have seen segmentation faults with 3.3.1 and openmpi when running
complex systems in parallel for systems that ran fine in serial. It
was certainly a head-scratcher as it did seem
Hello,
I am a new user of the free energy code. I am somewhat confused
regarding the method that should be applied to decouple the long range
interactions of the solvent from the solute while still maintaining
intramolecular long-range interactions for the solute.
I was able to find some
If your version is not current gromacs users always advise to
upgrade up to the last one.
Did you try to use mdp file from those systems which run correctly?
As for the last error, did it happen when you just reduce the number of
steps? It cannot be so...
I guess you may experience the problems
He, Yang wrote:
Hi Mark,
I just choose a small number of steps but it also does not work.it always shows
that
starting mdrun 'MODEL CYLINDER'
1 steps,300.0 ps.
Segmentation fault (core dumped)
OK, so that's a generic error message suggesting something is severely
wrong. Check the e
Hi Mark,
I just choose a small number of steps but it also does not work.it always shows
that
starting mdrun 'MODEL CYLINDER'
1 steps,300.0 ps.
Segmentation fault (core dumped)
I am not very sure about that.
Thank you .
Yang
From: gmx-users-bo
Try to copy grompp.mdp from the working system and start the run with
the problematic one. At least we will understand where to look for
the bug.
So what is the version of your gromacs, you didn't still answer.
HY> Hi, As for the version, I can get the trajectory file when I run
HY> other cases
Please keep all Gromacs-related correspondence on the users' list.
I do not have the time or resources to run jobs for you, nor do I typically open
attachments that I did not request. I did take a look at your structure file
and script, however, and I can tell you this much: running a 74,000-
He, Yang wrote:
I just tried it several times and still can not get the trajectory file. I am
using the 3.3.1 not new version but I can get the xtc or trr file when running
the other cases .
It seems unlikely you were able to run a million-step integration
several times to completion. Choose
I just tried it several times and still can not get the trajectory file. I am
using the 3.3.1 not new version but I can get the xtc or trr file when running
the other cases .
Yang
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Beha
gurgo> When I use the command "mdrun"to simulate the CG DNA model, I found that
all the files are output expect the trajectory file. I will list
gurgo> some parts of my mdp.file
What about another systems? Do they output the trajectory? What
version of gromacs do you use by the way? Do you run
He, Yang wrote:
yes, I mean that when using the command "mdrun", the traj.xtc file is not ouput at all
while the other files like "topol.tpr, ener.edr,md.log, mdout.mdp" are all output.
Well, neither topol.tpr nor mdout.mdp are produced by mdrun (they are produced
by grompp), so that doesn
yes, I mean that when using the command "mdrun", the traj.xtc file is not ouput
at all while the other files like "topol.tpr, ener.edr,md.log, mdout.mdp" are
all output.
Hence, I just got confused about that.
Yang
From: gmx-users-boun...@gromacs.org [gmx
He, Yang wrote:
I think this problem is not due to the disk space cause I check that it has a
large space in the fold. I have tried some times but always the same results
,no trajectory files while the others are normal .
What files are produced? And again, are you referring to the abse
I think this problem is not due to the disk space cause I check that it has a
large space in the fold. I have tried some times but always the same results
,no trajectory files while the others are normal .
Thank you very much for your reply.
Yang
From:
He, Yang wrote:
Hi all the users,
When I use the command "mdrun"to simulate the CG DNA model, I found that all
the files are output expect the trajectory file. I will list some parts of my mdp.file
During the simulation? Data is buffered, so you may not see immediate output.
Or is the
Hi all the users,
When I use the command "mdrun"to simulate the CG DNA model, I found that all
the files are output expect the trajectory file. I will list some parts of my
mdp.file
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit
Hi Steve,
what I intended to suggest was actually something different (and much easier).
The idea is not that you need some special system to be able to
utilize the pull code, but that the pull code is correct whereas the
g_dist and g_traj programs are not as good at treating pbc in the way
Actually I thought that if I don't exclude interactions, it would make mdrun
crash. I read in the mailing list that for using freeze option, I have to
exclude interactions, use comm_mode=none and use NVT conditions (although I
tried NPT too and it worked). Maybe I was missing something.
Thank
Hi,
Thank you Berk and Chris for the suggestions.
To address the possibility that this issue is related to periodic
boundaries, I used two approaches:
1. The pull group of interest (permeant) was centered in the x-y plane
of the box using Chris' approach. I then used the genconf utility to
Justin,
It great!
Vitaly
JAL> Vitaly Chaban wrote:
>> Hi,
>>
>> Is there a possibility to control g_energy output via command line
>> without interactive selection? I have found nothing about this in the
>> help message.
>>
>> We have a bunch of the alike systems, so we exactly know what numbe
Vitaly Chaban wrote:
Hi,
Is there a possibility to control g_energy output via command line
without interactive selection? I have found nothing about this in the
help message.
We have a bunch of the alike systems, so we exactly know what numbers
correspond to the wanted energy terms. If there
Vitaly Chaban wrote:
Hi,
Is there a possibility to control g_energy output via command line
without interactive selection? I have found nothing about this in the
help message.
We have a bunch of the alike systems, so we exactly know what numbers
correspond to the wanted energy terms. If there m
Hi,
Is there a possibility to control g_energy output via command line
without interactive selection? I have found nothing about this in the
help message.
We have a bunch of the alike systems, so we exactly know what numbers
correspond to the wanted energy terms. If there many alike systems it's
Hi,
For my test system it works with those modfications.
Can you file a bugzilla entry and attach all the files necessary
for running grompp?
Berk
> Date: Thu, 22 Jan 2009 21:48:41 -0500
> From: fied...@umich.edu
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Segmentation fault preprocessi
Hi,
No, if you need to freeze two proteins you do not have to exclude interactions.
Excluding interactions will make you simulation slightly faster,
but freeze groups freeze a group, even if there are forces working on it
(if there were no forces working, you would not need freeze groups in the f
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