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 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
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 iitd...@gmail.com
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 iitd...@gmail.com wrote:
Dear gmx users,
I had installed gromacs 4.6.1 using cmake. All
Thanks David. It worked.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Jun 5, 2013 at 1:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
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.
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
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
From: Justin A. Lemkul jalem...@vt.edu
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
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
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
-users] ngmx
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
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
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
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
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
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?
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
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
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 bharat.85.m...@gmail.comwrote:
I am trying to run the simulation trajectory using ngmx in windows .. but
it
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
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
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
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
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?) should
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
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
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
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
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
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
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
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
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
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 assume
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:
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 used it.
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 with some
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
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
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
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
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