[gmx-users] problem in ngmx

[Justin A. Lemkul]

Ms. Aswathy S wrote:
> Thank you very much for the reply...
> 
>  gmxcheck of my out shows a "segementation fault" in the last part. What could be the problem??
> 
> this is the last part of the output
> 
> x[31416] (-7.37978e-03  6.79718e+00  6.07531e+00) - (-7.40000e-03  6.79720e+00  6.07530e+00)
> x[31428] ( 2.35365e-01 -6.53947e-03  5.65519e+00) - ( 2.35400e-01 -6.50000e-03  5.65520e+00)
> x[31478] ( 1.54478e-02  6.14019e+00  5.74537e+00) - ( 1.54000e-02  6.14020e+00  5.74540e+00)
> Segmentation fault
> 
> 
> The energy minimisation & the equilibration steps are finished at 15 step eventhough it was given for 20 ps(10000 steps).But the output coordinates file doesnt show any abnornmality as i checked in the viewer? My equilibration step was in NVT.
> 
> whether nothing is happening or any other problem?
> 

If you got 15 steps when you expected 10000, it seems pretty clear to me that 
something crashed very early on in your simulation.

-Justin

> Thanks & regards,
> Aswathy
> 
> 
> 
> 
> Dept. Biotechnology
> Ext. 3108
> 
> ----- Original Message -----
> From: "Manik Mayur" <manik.mayur at gmail.com>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>, jalemkul at vt.edu
> Sent: Saturday, June 13, 2009 5:34:08 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
> Subject: Re: [gmx-users] problem in ngmx
> 
> 
> 
> 
> On Sat, Jun 13, 2009 at 5:14 PM, Florian Dommert < dommert at icp.uni-stuttgart.de > wrote: 
> 
> 
> * Justin A. Lemkul < jalemkul at vt.edu > [2009-06-13 07:31:17 -0400]: 
> 
> 
> 
> 
> 
> 
> Ms. Aswathy S wrote: 
> 
> 
> Hi, 
> 
> after equlibration of my protein and ligand I tried to create the energy file ans well as the to display the trajectories using ngmx option,. But it shows the follo: error, 
> 
> Xlib: connection to ":0.0" refused by server 
> Xlib: No protocol specified 
> 
> Can't connect to X Server. 
> Check your DISPLAY environment variable 
> 
> 
> Seems like your X environment is somehow not properly configured. 
> 
> 
> If you are working through ssh, then you can : 
> 
> $export DISPLAY=<your current computer's ip>:0.0 
> 
> 
> 
> Or you are tunneling through a SSH connection. There are several 
> possiblities: 
> 
> 1. Try ssh -X to login, this could solve the problem, if you are in 
> principle allowed to use X11 tunneling. 
> 2. In case this does not work either it can be that you are not allowed 
> to tunnel X11. 
> 
> However take care that you also need a properly configured XServer 
> running on your own system not just on the host you login. So in case 
> you use Windows or MacOS make sure this is the case. 
> 
> Flo 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ************************************************ 
> 
> also the g_energy command shows that , 
> 
> Program g_energy_mpi, VERSION 3.3.3 
> Source code file: enxio.c, line: 239 
> 
> Fatal error: 
> Energy file eq_2ps_ener.edr not recognized, maybe different CPU? 
> 
> 
> What does gmxcheck tell you about the file. Perhaps it has been corrupted in some way. 
> 
> Also, you may want to work with a more current version (4.0.5) to utilize the newest features and bug fixes. 
> 
> -Justin 
> 
> 
> 
> 
> Can any one help me, please??? 
> 
> Thanks, 
> Aswathy 
> ASBT 
> Dept. Biotechnology 
> Ext. 3108 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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