Re: [gmx-users] problem in ngmx

2009-06-17 Thread Ms. Aswathy S
: Wednesday, June 17, 2009 6:35:01 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Marc F. Lensink wrote: > On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote: >> The .mdp file seems reasonable. QM charges are not necessarily

Re: [gmx-users] problem in ngmx

2009-06-17 Thread Justin A. Lemkul
Marc F. Lensink wrote: On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote: The .mdp file seems reasonable. QM charges are not necessarily the end result in Gromos parameterization. In fact, such calculations are often unnecessary. In my experience, assigning charges based on f

Re: [gmx-users] problem in ngmx

2009-06-17 Thread Marc F. Lensink
On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote: > > The .mdp file seems reasonable. QM charges are not necessarily the end > result in Gromos parameterization. In fact, such calculations are often > unnecessary. In my experience, assigning charges based on functional groups >

Re: [gmx-users] problem in ngmx

2009-06-17 Thread Justin A. Lemkul
- Original Message - From: "Justin A. Lemkul" To: "Gromacs Users' List" Sent: Tuesday, June 16, 2009 5:29:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: My point was I have set the NVT equilibration

Re: [gmx-users] problem in ngmx

2009-06-16 Thread Ms. Aswathy S
. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Gromacs Users' List" Sent: Tuesday, June 16, 2009 5:29:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > My

Re: [gmx-users] problem in ngmx

2009-06-16 Thread Justin A. Lemkul
; you need to figure out why. -Justin Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Gromacs Users' List" Sent: Tuesday, June 16, 2009 5:03:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] probl

Re: [gmx-users] problem in ngmx

2009-06-16 Thread Ms. Aswathy S
rs' List" Sent: Tuesday, June 16, 2009 5:03:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > sorry..forgot to attach the file... > > After my NVT I have checked the PE of the system..It was stabilised..So I >

Re: [gmx-users] problem in ngmx

2009-06-16 Thread Justin A. Lemkul
nt: Tuesday, June 16, 2009 4:44:47 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: Hi, In my NPT step I think there is some poblem. i am getting the follo: error. I have used box as cubic I s that could be the problem Plea

Re: [gmx-users] problem in ngmx

2009-06-16 Thread Ms. Aswathy S
- From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Tuesday, June 16, 2009 4:44:47 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > Hi, > > In my NPT step I think there is

Re: [gmx-users] problem in ngmx

2009-06-16 Thread Justin A. Lemkul
eefheart) OIn some pev Dept. Biotechnology Ext. 3108 - Original Message - From: "Ms. Aswathy S" To: "Discussion list for GROMACS users" Sent: Tuesday, June 16, 2009 12:40:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx

Re: [gmx-users] problem in ngmx

2009-06-16 Thread Justin A. Lemkul
- Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Monday, June 15, 2009 4:58:20 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: Hi Justin, Thanks for the

Re: [gmx-users] problem in ngmx

2009-06-16 Thread Ms. Aswathy S
; (Captain Beefheart) OIn some pev Dept. Biotechnology Ext. 3108 - Original Message - From: "Ms. Aswathy S" To: "Discussion list for GROMACS users" Sent: Tuesday, June 16, 2009 12:40:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] pro

Re: [gmx-users] problem in ngmx

2009-06-16 Thread Ms. Aswathy S
2009 4:58:20 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > Hi Justin, > > Thanks for the reply. > > Once again i tried to minimize the protein +ligand in vacuum. Also tried by > varying the maximum force c

Re: [gmx-users] problem in ngmx

2009-06-15 Thread Justin A. Lemkul
" Sent: Sunday, June 14, 2009 10:51:30 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: Hi Justin, I tried maximum to find out the problem but i failed in that. I will give you the detailed steps..Kindly check once and t

Re: [gmx-users] problem in ngmx

2009-06-14 Thread Ms. Aswathy S
- From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Sunday, June 14, 2009 10:51:30 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > Hi Justin, > > I tried maximum to find ou

Re: [gmx-users] problem in ngmx

2009-06-14 Thread Justin A. Lemkul
4 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx 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

Re: [gmx-users] problem in ngmx

2009-06-14 Thread Ms. Aswathy S
lease find some time to help me. Thank you very much, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Saturday, June 13, 2009 6:23:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi

Re: [gmx-users] problem in ngmx

2009-06-13 Thread Justin A. Lemkul
+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: H

Re: [gmx-users] problem in ngmx

2009-06-13 Thread Ms. Aswathy S
"Manik Mayur" To: "Discussion list for GROMACS users" , 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.d

Re: [gmx-users] problem in ngmx

2009-06-13 Thread Jussi Lehtola
On Sat, 2009-06-13 at 17:34 +0530, Manik Mayur wrote: > Seems like your X environment is somehow not properly > configured. > > If you are working through ssh, then you can : > > $export DISPLAY=:0.0 Ugh, that's the archaic, telnet epoch way of doing it. It doesn

Re: [gmx-users] problem in ngmx

2009-06-13 Thread Manik Mayur
On Sat, Jun 13, 2009 at 5:14 PM, Florian Dommert < domm...@icp.uni-stuttgart.de> wrote: > * Justin A. Lemkul [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

Re: [gmx-users] problem in ngmx

2009-06-13 Thread Florian Dommert
* Justin A. Lemkul [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 serv

Re: [gmx-users] problem in ngmx

2009-06-13 Thread Justin A. Lemkul
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

[gmx-users] problem in ngmx

2009-06-13 Thread Ms. Aswathy S
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 DISPLA