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
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
gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Friday, January 23, 2009 12:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
> I just tried it seve
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
Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 12:09 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
> yes, I mean that when using the command "mdrun", the traj.xtc file is not
> ouput at all
-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 11:55 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
I think this problem is not due to the disk spa
-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 11:55 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
> I think this problem is not due to the disk spa
[jalem...@vt.edu]
Sent: Friday, January 23, 2009 11:42 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] why the trajectory file is not output
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
: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 11:42 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
> Hi all the users,
>
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
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