: 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
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
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
>
- 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
. 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
; 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
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
>
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
-
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
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
- 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
; (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
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
" 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
-
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
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
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
+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
"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
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
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
* 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
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
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.
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