[gmx-users] why the trajectory file is not output

2009-01-23 Thread chris . neale
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

Re: [gmx-users] why the trajectory file is not output

2009-01-23 Thread Mark Abraham
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

RE: [gmx-users] why the trajectory file is not output

2009-01-23 Thread He, Yang
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

Re: [gmx-users] why the trajectory file is not output

2009-01-23 Thread Mark Abraham
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

RE: [gmx-users] why the trajectory file is not output

2009-01-23 Thread He, Yang
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

Re: [gmx-users] why the trajectory file is not output

2009-01-23 Thread Justin A. Lemkul
-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

RE: [gmx-users] why the trajectory file is not output

2009-01-23 Thread He, Yang
-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

Re: [gmx-users] why the trajectory file is not output

2009-01-23 Thread 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, When I use the command "mdrun"to simulate the CG DNA model, I found that all the files

RE: [gmx-users] why the trajectory file is not output

2009-01-23 Thread He, Yang
: 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, >

Re: [gmx-users] why the trajectory file is not output

2009-01-23 Thread Justin A. Lemkul
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

[gmx-users] why the trajectory file is not output

2009-01-23 Thread He, Yang
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