Thanks David. It worked.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Jun 5, 2013 at 1:02 AM, Dr. Vitaly Chaban wrote:
> I do not know about the newest versions, but in older ones ngmx was missed
> when you did not have the lesstif library installed.
>
>
> Dr. Vitaly Chaban
>
>
I do not know about the newest versions, but in older ones ngmx was missed
when you did not have the lesstif library installed.
Dr. Vitaly Chaban
On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury wrote:
> Dear gmx users,
>
> I had installed gromacs 4.6.1 using cmake. All the binaries are
This has been default behaviour for years. See pre-conditions here
http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_3.5._Optional_build_components.
David's email has one way to solve the problem.
Mark
On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury wrote:
> Dear gmx use
On 2013-06-04 17:55, Chandan Choudhury wrote:
Dear gmx users,
I had installed gromacs 4.6.1 using cmake. All the binaries are installed,
but surprisingly I do not find ngmx executable. Can anyone guide me how do
I install ngmx using cmake.
cmake -DGMX_X11=ON
Chandan
--
Chandan kumar Choudhur
Dear gmx users,
I had installed gromacs 4.6.1 using cmake. All the binaries are installed,
but surprisingly I do not find ngmx executable. Can anyone guide me how do
I install ngmx using cmake.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
gmx-users mailing listgmx-users@gromacs.org
On 2/20/13 12:46 AM, Hector Manuel Manzanilla Granados wrote:
Excuseme dear Dr. Tomas, forgiveme the boldness,
I'm new with this, and I dont know who to address
when I have a problem. My name is Hector, and I'm
tryng to install the gromacs software in my computer;
I follewed all the steps in t
Dear Justin,
Thank you very much from your response.
Best Regards
Sara
From: Justin A. Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Sent: Tuesday, May 8, 2012 6:15 AM
Subject: Re: [gmx-users] ngmx
On 5/7/12 9:42 PM, mohammad agha wrote
On 5/7/12 9:42 PM, mohammad agha wrote:
Dear Justin,
Thank you very much from your reply.
I installed VMD on my system before but when I type vmd in terminal, the basic
page of VMD flash and disappear!!! Because of my system was sensitive So, I
decided work by ngmx. Can you help me about this
From: Justin A. Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Sent: Monday, May 7, 2012 10:28 PM
Subject: Re: [gmx-users] ngmx
On 5/7/12 1:50 PM, mohammad agha wrote:
> Dear Gromacs users,
>
> I work with Gromacs in Linux, I want
On 5/7/12 1:50 PM, mohammad agha wrote:
Dear Gromacs users,
I work with Gromacs in Linux, I want prepare a copy of snapshots by ngmx with
jpg or pdf format or whatever that be open in Windows.
May I ask you to help me,Please?
ngmx is a very simple viewing program. There are far better rend
Dear Gromacs users,
I work with Gromacs in Linux, I want prepare a copy of snapshots by ngmx with
jpg or pdf format or whatever that be open in Windows.
May I ask you to help me,Please?
Best Regards
Sara
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinf
Thomas Koller wrote:
Hello!
Why does the animation with ngmx not work always properly?
You'll have to define the symptoms better to get an answer to this. ngmx is a
very (very) rudimentary viewing program. You're better off with something more
sophisticated, like VMD or PyMol.
How
Hello!
Why does the animation with ngmx not work always properly?
How can I save the animation in Linux?
Thanks!
Thomas
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lis
On 31/01/2011 11:34 AM, Justin A. Lemkul wrote:
gromacs wrote:
Hi Everyone,
Program ngmx, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708
Fatal error:
reading tpx file (md1.tpr) version 73 with version 58 program
I installed 4.0.7 before, and now i installed 4.5.3.
On 31/01/2011 11:15 AM, gromacs wrote:
Hi Everyone,
Program ngmx, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708
Fatal error:
reading tpx file (md1.tpr) version 73 with version 58 program
I installed 4.0.7 before, and now i installed 4.5.3. How can i use
ngmx now?
gromacs wrote:
Hi Everyone,
Program ngmx, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708
Fatal error:
reading tpx file (md1.tpr) version 73 with version 58 program
I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now?
You need a compati
Hi Everyone,
Program ngmx, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708
Fatal error:
reading tpx file (md1.tpr) version 73 with version 58 program
I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now?
The second question is running C2H5OH
No i did not --disbale-x in your configuration ... I was not having that
library but now i installed the library now ..
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -6
On 11/11/2010 3:03 PM, bharat gupta wrote:
I am trying to run the simulation trajectory using ngmx in windows ..
but it seems that the ngmx.exe file doesnot exists .. can anybody tell
what shall i do to view the movie of my simulation
Did you --disable-x in your configuration? Do you have the
If you compile using cygwin than it should be able to compile ngmx if you
have all required X11 libraries. I recommend you to use VMD.
On Wed, Nov 10, 2010 at 11:03 PM, bharat gupta wrote:
> I am trying to run the simulation trajectory using ngmx in windows .. but
> it seems that the ngmx.exe fil
I am trying to run the simulation trajectory using ngmx in windows .. but it
seems that the ngmx.exe file doesnot exists .. can anybody tell what shall i
do to view the movie of my simulation
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of
On Tue, 24 Jun 2008 11:24:46 +0300
Vitaly Chaban <[EMAIL PROTECTED]> wrote:
Xavier,
Thank for a clarification.
Don't you have any ideas why 'ngmx' can have display->filter dialog
inactive? Except the case when index-file in wrong-formatted?
No idea! Never used ngmx. Although it seems to be us
Xavier,
Thank for a clarification.
Don't you have any ideas why 'ngmx' can have display->filter dialog
inactive? Except the case when index-file in wrong-formatted?
XP> On Tue, 24 Jun 2008 10:26:27 +0300
XP> Vitaly Chaban <[EMAIL PROTECTED]> wrote:
>> What numbers (of molecules or of atoms?)
On Tue, 24 Jun 2008 10:26:27 +0300
Vitaly Chaban <[EMAIL PROTECTED]> wrote:
What numbers (of molecules or of atoms?) should contain 'index.ndx' in
atoms
"ngmx -n index.ndx" ?
When using 'index.ndx' with molecules numbers it seems to read it as
those of atoms and when using 'index.ndx' with
What numbers (of molecules or of atoms?) should contain 'index.ndx' in
"ngmx -n index.ndx" ?
When using 'index.ndx' with molecules numbers it seems to read it as
those of atoms and when using 'index.ndx' with atoms it just refuses
to start (the section appeared in display->filter is inactive, I
Dear gmx-users,
I have installed the gromacs 3.3.3 on a dual core HP workstation with
Ubuntu platform. All the programs are properly installed and working
except ngmx and dssp. However there is a difference, ngmx is not
installed as I donot see the link in /usr/local/bin along with the
oth
Dear gmx-users,
I have installed the gromacs 3.3.3 on a dual core HP workstation with Ubuntu
platform. All the programs are properly installed and working except ngmx and
dssp. However there is a difference, ngmx is not installed as I donot see the
link in /usr/local/bin along with the other pr
sharada wrote:
To get ngmx working, you need to refrain from disabling X support on
your GROMACS configure command line, and to have a suitable X and Motif
library installed and working and findable by the GROMACS configure.
I have installed the gromacs 3.3.3 on a dual core HP workstation wit
Dear gmx-users,
I have installed the gromacs 3.3.3 on a dual core HP workstation with Ubuntu
platform. All the programs are properly installed and working except ngmx and
dssp. However there is a difference, ngmx is not installed as I donot see the
link
jayant james wrote:
Hi!
I am trying to get the intermediate structures from a 2ns simulation and
I use ngmx for the same. I am able to open the visualizer using the command
ngmx -f trj.trr -s pr.tpr
But when I try to get the coordinate file (say 50ps) I get an error as
given below. How am I to
On May 8, 2008, at 2:09, jayant james wrote:
Hi!
I am trying to get the intermediate structures from a 2ns
simulation and I use ngmx for the same. I am able to open the
visualizer using the command
ngmx -f trj.trr -s pr.tpr
But when I try to get the coordinate file (say 50ps) I get an error
Hi!
I am trying to get the intermediate structures from a 2ns simulation and I
use ngmx for the same. I am able to open the visualizer using the command
ngmx -f trj.trr -s pr.tpr
But when I try to get the coordinate file (say 50ps) I get an error as given
below. How am I to overcome this problem ?
Hi,
On Oct 13, 2007, at 6:04 PM, Sagittarius wrote:
I already have some kind of cygwin.
Could you please provide me with more details on
"install cygwin with some kind of X server"
Thank you in advance
Actually, if you don't absolutely need ngmx you can just disable the
X11-dependent parts
Thank you very much
"Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: When you run the setup.exe for
Cygwin, install the X11 package.
Quoting David van der Spoel :
> Sagittarius wrote:
> > I already have some kind of cygwin.
> > Could you please provide me with more details on
> > "install cygwin
When you run the setup.exe for Cygwin, install the X11 package.
Quoting David van der Spoel <[EMAIL PROTECTED]>:
> Sagittarius wrote:
> > I already have some kind of cygwin.
> > Could you please provide me with more details on
> > "install cygwin with some kind of X server"
> no, I have never use
Sagittarius wrote:
I already have some kind of cygwin.
Could you please provide me with more details on
"install cygwin with some kind of X server"
no, I have never used it.
check the wiki.
Thank you in advance
*/David van der Spoel <[EMAIL PROTECTED]>/* wrote:
Sagittarius wrote:
>
I already have some kind of cygwin.
Could you please provide me with more details on
"install cygwin with some kind of X server"
Thank you in advance
David van der Spoel <[EMAIL PROTECTED]> wrote:
Sagittarius wrote:
> Dear Gromacs users,
>
> I am trying to compile ngmx part of Gromacs (I ass
Sagittarius wrote:
Dear Gromacs users,
I am trying to compile ngmx part of Gromacs (I assume grphics).
Visual studio linking gives error messages including:
xutil.obj : error LNK2001: unresolved external symbol _XLookupString
xutil.obj : error LNK2001: unresolved external symbol
_XChangeWin
Dear Gromacs users,
I am trying to compile ngmx part of Gromacs (I assume grphics).
Visual studio linking gives error messages including:
xutil.obj : error LNK2001: unresolved external symbol _XLookupString
xutil.obj : error LNK2001: unresolved external symbol _XChangeWindowAttributes
x
sharada wrote:
Dear Mark Abraham,
Thanks a lot for the help. I am sorry about the subject line . I just
overlooked it. Regarding ngmx I would try to configure again and check
for the errors. That means I would have to go through the process all
over again. What are the required libraries
sharada wrote:
Dear Mark Abraham,
Thanks a lot for the help. I am sorry about the subject line . I just
overlooked it. Regarding ngmx I would try to configure again and check
for the errors. That means I would have to go through the process all
over again. What are the required libraries
Dear Mark Abraham,
Thanks a lot for the help. I am sorry about the subject line . I just
overlooked it. Regarding ngmx I would try to configure again and check
for the errors. That means I would have to go through the process all
over again. What are the required libraries ?
regards
shar
i think since i do not have cell as of now.. i.e with 0.5 0.5 0.5 cell
size and also with 1.0 1.0 1.0 cell size , gromacs is not able to
generate pbc.On 5/11/06, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Karam,If you think you know why, please share your thoughts.. that can help us provide an ans
the problem continues even if i rescale my box to 1.0 1.0 1.0 :(On 5/11/06, karamyog singh <[EMAIL PROTECTED]
> wrote:hmm.. i know about the no. of atoms in bcc. please tell me what to do if i want more than 1 unit cell?
gromacs is not supporting periodic boundary conditions for my cell and i think
Karam,If you think you know why, please share your thoughts.. that can help us provide an answer.Still, gromacs supports all periodic boundary conditions, except for real exotic stuff like spherical (and I can think of a few others). But any crystal packing can be handled. Maybe the easiest for you
hmm.. i know about the no. of atoms in bcc. please tell me what to do if i want more than 1 unit cell?gromacs is not supporting periodic boundary conditions for my cell and i think i know y.
On 5/11/06, Mark Abraham <[EMAIL PROTECTED]> wrote:
karamyog singh wrote:> Thnx Mark. I stil have a doubt. I
Hi Karamyog,First build the crystal consisting of the number of atoms you want to include, using the crystal lattice vectors. Than build your unit cell as to contain these. Again use the crystal lattice vectors, but scale them for the size of your crystal unit cell. So, if your crystal is 10x10x10
karamyog singh wrote:
Thnx Mark. I stil have a doubt. If want to simulate a crystal
structure,then how should i go about it? wht changes should be made in
the above file? even if i replace the 27th atom with 0.5 0.25 0.5, then
too it will overlay some other atom.
0.5 == 0 if the size is 0.5.
Thnx Mark. I stil have a doubt. If want to simulate a crystal
structure,then how should i go about it? wht changes should be made in
the above file? even if i replace the 27th atom with 0.5 0.25 0.5, then
too it will overlay some other atom.
I understand wht the fault with my conf.gro file is, but
karamyog singh wrote:
Respected gentlemen, I have written another code for simulating atomic
oxygen. the code is running fine. however when i view my run using ngmx,
the entire box doesn't get filled up.It just shows one plane of atoms. I
have a box of 27 atoms but ngmx shows only 9. Can any1 t
Respected gentlemen, I have written another code for simulating atomic
oxygen. the code is running fine. however when i view my run using
ngmx, the entire box doesn't get filled up.It just shows one plane of
atoms. I have a box of 27 atoms but ngmx shows only 9. Can any1 tell me
why and the solutio
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