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.ma...@gmail.com> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>, jalem...@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 < domm...@icp.uni-stuttgart.de > wrote: * Justin A. Lemkul < jalem...@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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== 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 ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !! _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
