[gmx-users] problem in ngmx

Sat Jun 13 14:36:19 CEST 2009

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?

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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-- 
Florian Dommert 
Dipl.-Phys. 

Institute for Computational Physics 
University Stuttgart 

Pfaffenwaldring 27 
70569 Stuttgart 

Tel: +49 - 711 / 6856-3613 
Fax: +49 - 711 / 6856-3658 

EMail: dommert at icp.uni-stuttgart.de 
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert 

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Manik Mayur 
Graduate student 
Microfluidics Lab 
Dept. of Mechanical Engg. 
IIT Kharagpur 
INDIA 

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