On Feb 25, 1:30 pm, Patrick Kiley pjki...@gmail.com wrote:
Could not link against GROMACS, please choose libraries to link
against with --with-libgmx=XXX
or specify it in GMX_LIBS (e.g. export GMX_LIBS=-Lgromacs-path/lib -
lgmx)
or disable GROMACS support with --without-libgmx.
I set
attached the config.log from the configure run of csg to this email.
Thank you
Nikos
On Sat, Feb 26, 2011 at 4:51 PM, Christoph Junghans
jungh...@mpip-mainz.mpg.de wrote:
Hi Nikos,
Hello,
I am trying to install VOTCA 1.1 on a guest machine for which I don't
have root access and I am
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and managed to solve
it, i will be very grateful if someone can help me.
Best regards,
Sacha
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-1.1.2/lib/libvotca_tools.so, not found
(try using -rpath or -rpath-link)
On Fri, Jun 24, 2011 at 2:55 PM, Christoph Junghans
jungh...@mpip-mainz.mpg.de wrote:
2011/6/24 Nikos Bentenitis bente...@southwestern.edu:
This is a followup to my last question: I found out that there is an
option
:
In this case I have to multiply x value (rad) on (180/3.14) and
afterwords I can use this distribution function for getting the
potential and if it's not zero just simply shift it to zero?
On Jun 27, 3:20 pm, Christoph Junghans jungh...@votca.org wrote:
You can shift the minimum to zero
chemistry donets1...@gmail.com:
In this case I have to multiply x value (rad) on (180/3.14) and
afterwords I can use this distribution function for getting the
potential and if it's not zero just simply shift it to zero?
On Jun 27, 3:20 pm, Christoph Junghans jungh...@votca.org wrote
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'min' in seetings.xml to a value
unequal 0 (in your case 0.33 or so) to prevent VOTCA from calculating
an update in the region r min.
Cheers,
Christoph
Thanks a lot in advance,
Sergio
On Jul 16, 4:42 pm, Christoph Junghans jungh...@votca.org wrote:
2011/7/16 chemistry donets1
@milano:~/VOTCA-play_around$
I have also tried running mmdrun before submitting for the iterations
and it was running. (Going to try in the step 001 now)
On Aug 18, 4:07 pm, Christoph Junghans jungh...@votca.org wrote:
Hi Valentina,
have a look at inverse.log to see if and how mdrun
:
Great, thanks!
I will try it tomorrow:)
V
On Aug 18, 8:10 pm, Christoph Junghans jungh...@votca.org wrote:
Hi Valentina,
it seems you are a bug hunter ;-)
I just found the problem in build.sh, just run ./build.sh --selfupdate
'./build.sh --dev XXX' builds the development version
]: *** [cmTryCompileExec] Error 1
gmake[1]: Leaving directory `/opt/votca/src/tools/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec/fast] Error 2
On Aug 19, 1:47 pm, Christoph Junghans jungh...@votca.org wrote:
Hmm, I have not tested fftw 3.3, it must be super new.
Can you post the part of your CMakeError.log
Hi Marc,
malloc.h is usually a part of the libc, so possibly you have to
install the libc's development package.
Under linux that is usually called glibc-dev or glibc-devel.
Cheers,
Christoph
2011/8/22 Marc-André Dubois ma.dub...@umontreal.ca:
Hi guys,
I tried to install
/ to the cmake (or build.sh)
command.
Cheers,
Christoph
2011/8/23 Marc-André Dubois ma.dub...@umontreal.ca:
Thanks Christoph. I'm running osx, libc should be already installed…
Marc
Le 2011-08-22 à 17:42, Christoph Junghans a écrit :
Hi Marc,
malloc.h is usually a part of the libc, so
Dear all,
Votca 1.2.1 was released as a lot of small bug fixes have accumulated:
https://code.google.com/p/votca/source/browse/share/CHANGELOG.t2t?repo=csgname=stable
The most important change fixed roundoff problem in the grid search.
Cheers,
Christoph
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On Aug 5, 8:08 pm, Valentina valentina_erast...@yahoo.co.uk wrote:
Awesome! Thank you very much, editing PKG_CONFIG_PATH did the trick!
V
On Aug 5, 7:20 pm, Christoph Junghans jungh...@votca.org wrote:
Hi Valentina,
You can have a look at CMakeFiles
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with
-- package 'libgmx_d' not found
From your email above.
What kind of error does csg/CMakeFiles/CMakeError.log report at the end?
Christoph
Patrick
On Tue, Oct 11, 2011 at 4:24 PM, Christoph Junghans jungh...@votca.org
wrote:
Am 11. Oktober 2011 17:05 schrieb Patrick Kiley pjki
?
patrick
On Tue, Oct 11, 2011 at 5:17 PM, Christoph Junghans jungh...@votca.org
wrote:
Am 11. Oktober 2011 18:08 schrieb Patrick Kiley pjki...@gmail.com:
Here is the contents of the entire file:
Determining if the function GromacsVersion exists in the
/usr/local/gromacs/lib
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gromacs commands and direct its output to dump file, and in
the end delete the dump file.
what do you think?
thanks
sikandar
On Thu, Oct 20, 2011 at 3:49 AM, Christoph Junghans jungh...@votca.org
wrote:
hi,
yes no.
On the one hand the default of all gromacs tools is to print
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see below, one attched file ,
GROMACS_LIBRARY output as well as gmx_version.
seems to be a problem between gromacs dowloaded version and gromacs
version used by votca.
Best Regards
Marc
On Tue, Nov 1, 2011 at 5:45 PM, Christoph Junghans jungh...@votca.org wrote:
Am 21. Oktober 2011 14:27
is 1.7.6 build.sh version.
#version 1.7.6 -- 14.10.11 do clean by default again
On Wed, Nov 2, 2011 at 11:08 PM, Christoph Junghans jungh...@votca.org
wrote:
Hi Marc,
Are you using the latest version of build.sh? (currently 1.7.6)
Cheers,
Christoph
Am 1. November 2011 15:16 schrieb
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And yes, this is a bug: https://code.google.com/p/votca/issues/detail?id=121
Christoph
Am 9. November 2011 02:52 schrieb Sacha Mould sacha...@gmail.com:
Hi Christoph,
it works Thanks so much
All the best,
Sacha
On Nov 9, 3:19 am, Christoph Junghans jungh...@votca.org wrote
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thanks
sikandar
On Sat, Nov 26, 2011 at 4:44 PM, Christoph Junghans jungh...@votca.org
wrote:
Am 26. November 2011 14:26 schrieb Sikandar Mashayak
symasha...@gmail.com:
I am trying to install Votca with mpi enabled gromacs. And it is not
able to
link to
gromacs since library file name
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On Dec 15, 7:50 pm, Christoph Junghans jungh...@votca.org wrote:
Hi rp,
which version of cmake is it?
$cmake --version
Please add the '--debug' option and attach the output.
Cheers,
Christoph
Am 15. Dezember 2011 11:42 schrieb rp rakheep...@gmail.com:
Dear Users,I get
Thanks for your time. I appreciate
On Dec 15, 10:00 pm, Christoph Junghans jungh...@votca.org wrote:
Just run:
$ ./build.sh --debug -prefix ${prefix} --latest tools csg
Am 15. Dezember 2011 19:46 schrieb rp rakheep...@gmail.com:
This is cmake 2.8.6 and I am installing votca
):
src/libtools/CMakeLists.txt:11 (find_package)
-- Configuring incomplete, errors occurred!
Thanks, I appreciate
On Dec 16, 11:24 am, Christoph Junghans jungh...@votca.org wrote:
Please read:
http://code.google.com/p/votca/wiki/Installing#From_Source
As described there, you need to add
.
make[1]: Leaving directory `/home/rp/src/tools/CMakeFiles/CMakeTmp'
make: *** [cmTryCompileExec/fast] Error 2
Thank you
Rakhee
On Dec 17, 5:12 pm, Christoph Junghans jungh...@votca.org wrote:
Can you please post /home/rp/src/tools/CMakeFiles/CMakeError.log?
Am 17. Dezember 2011 13:22
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-BBA_a2.xvg table-BAB_a3.xvg table-BBC_a4.xvg table-DBBA_d1.xvg
table-BBAB_d2.xvg table-ABBC_d3.xvg table-ABBA_d4.xvg/filelist
You can do multiple filelist options or just add a newline if you want.
Christoph
Thanks,
Tinashe
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If have added a fix in the buildutil, please update.
Christoph
Thanks All
Rakhee
On Sun, Dec 18, 2011 at 11:09 AM, Christoph Junghans jungh
gromacs
Thanks.
Tinashe
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On Feb 15, 6:37 pm, Christoph Junghans jungh...@votca.org wrote:
Am 15. Februar 2012 09:58 schrieb Tinashe tinashe.nd...@gmail.com: (Error
1)
$ awk -v kbt=1.6629 '{print $1, -kbt*log($2/$1/$1)}'
bond.dist.resample bond.pot.ib
awk: (FILENAME
, Christoph Junghans jungh...@votca.org wrote:
Am 15. Februar 2012 13:39 schrieb Rakhee Pani rakheep...@gmail.com: I am
getting some error message related to fftw libraries .
91%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/parsexml.cc.o
[ 95%] Building CXX object
src/libtools
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at 8:42 PM, Christoph Junghans jungh...@votca.org
wrote:
Hi karteek,
you will not get an answer faster if you ask 3 times, this will
actually have the opposite effect :-)
The support for LAMMPS in VOTCA is very basic, which means all VOTCA
analysis tools (csg_*) can read LAMMPS dump files
,
Christoph
2012/8/27 Andrew Jewett jewett@gmail.com:
On Monday, August 27, 2012 11:12:54 AM UTC-4, Christoph Junghans wrote:
On the other hand the only reason to use LAMMPS with VOTCA would be if
you want to use feature, which is not implemented in Gromacs. IBI on
non-bonded 3-body interactions
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You received this message because you
own code already;) but I was hoping I can
do it within Votca.
Have a good weekend,
Valentina
On Friday, September 28, 2012 6:05:02 PM UTC+1, Christoph Junghans wrote:
Hi,
2012/9/28 Valentina valentina...@yahoo.co.uk:
Hello!
I am a little confused here.
I have read somewhere
with
--cg option once by hand to see if the distributions are calculated
correctly.
Christoph
2012/10/17 Valentina valentina_erast...@yahoo.co.uk:
Ok, great. I will try the tutorial and see where I have gone wrong.
On Wednesday, October 17, 2012 6:15:02 PM UTC+1, Christoph Junghans wrote
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using gromacs.equi_time in the settings file
Good luck!
-Sebastian
Zitat von Christoph Junghans jungh...@votca.org:
Hi,
2012/10/31 Anu Nagarajan anu.naga...@gmail.com:
Hi,
I am trying to run the thermodynamic force using csg_inverse. I have the
settings.xml file with appropriate options
2012/11/28 ms deviceran...@gmail.com:
On 28/11/12 01:49, Christoph Junghans wrote:
2012/11/24 ms deviceran...@gmail.com:
[snip]
It is hard to derive what went wrong, but you could try:
- run mdrun on 1 core only
- run the same simulation with adress=no on 8 cores
- export GMX_NB_GENERIC
.
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${beads[$i]}-${beads[$j]}.dist.tgt/target
gromacs
tabletable_${beads[$i]}_${beads[$j]}.xvg/table
/gromacs
/inverse
/non-bonded
EOF
done
done
echo /cg
Thank you very much for your time.
Cheers,
Davide
On 25/03/13 4:38 PM, Christoph Junghans jungh...@votca.org
/opt_out.
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HANASAKI hanas...@me.es.osaka-u.ac.jp:
Dear Dr. Christoph Junghans
(CC: VOTCA development team)
We had received a reply from you some time ago as follows, and I would like
to know
some more specific information on how to use the data of radial distribution
funciton
as the only(?) input
2013/5/30 s.neuman...@gmail.com:
Whats the name of this software?
I do not have this variable defined...
I just meant the shell command xmlwf, it comes with expat, which you
need for VOTCA anyhow.
On Wednesday, May 29, 2013 4:26:54 PM UTC+1, Christoph Junghans wrote:
2013/5/29 s.neu
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2013/7/1 s.neuman...@gmail.com:
W dniu poniedziałek, 1 lipca 2013 02:51:23 UTC+1 użytkownik Christoph
Junghans napisał:
2013/6/18 s.neu...@gmail.com:
Dear Votca Users,
I have started using the software some time ago and i successfully
managed
to extract bonded parameters from
an
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2013/7/1 s.neuman...@gmail.com:
W dniu poniedziałek, 1 lipca 2013 15:04:38 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/1 s.neu...@gmail.com:
W dniu poniedziałek, 1 lipca 2013 02:51:23 UTC+1 użytkownik Christoph
Junghans napisał:
2013/6/18 s.neu...@gmail.com:
Dear
2013/7/1 s.neuman...@gmail.com:
W dniu poniedziałek, 1 lipca 2013 15:09:12 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/1 s.neu...@gmail.com:
I am trying to run IBI for angles. I calculated 88 distributions for
angles
(its a protein made of 90 beads) using csg_boltzmann
2013/7/1 s.neuman...@gmail.com:
W dniu poniedziałek, 1 lipca 2013 16:27:04 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/1 s.neu...@gmail.com:
W dniu poniedziałek, 1 lipca 2013 15:28:35 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/1 s.neu...@gmail.com:
W
2013/7/2 s.neuman...@gmail.com:
On Monday, July 1, 2013 5:09:27 PM UTC+1, Christoph Junghans wrote:
2013/7/1 s.neu...@gmail.com:
W dniu poniedziałek, 1 lipca 2013 16:27:04 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/1 s.neu...@gmail.com:
W dniu poniedziałek, 1
at http://groups.google.com/group/votca.
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Christoph Junghans
Web: http://www.compphys.de
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the updated conf.esp.gz from:
https://csg-tutorials.votca.googlecode.com/hg/methanol/ibi_espresso/conf.esp.gz
Christoph
Best Regards!
Zhicheng
在 2013年6月28日星期五UTC+8下午10时49分24秒，Christoph Junghans写道：
2013/6/28 Zhicheng zcgu...@gmail.com:
Dear all:
The hist (tab) command within
a gromacs specialty.
Christoph
Sincerely,
Zhicheng
2013/7/3 Christoph Junghans jungh...@votca.org
2013/7/3 Zhicheng zcguo1...@gmail.com:
Hi Christoph,
I retried the methanol/ibi_espresso tutorial and modified the bead
interaction of lennard-jones (inter 0 0 lennard-jones
...@googlegroups.com.
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On Monday, July 8, 2013 10:26:41 PM UTC+1, Christoph Junghans wrote:
2013/7/8 s.neu...@gmail.com:
W dniu poniedziałek, 8 lipca 2013 18:00:32 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/8 s.neu...@gmail.com:
W dniu poniedziałek, 8 lipca 2013 16:44:20 UTC+1 użytkownik
PM UTC+1, Christoph Junghans wrote:
2013/7/8 s.neu...@gmail.com:
W dniu poniedziałek, 8 lipca 2013 18:00:32 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/8 s.neu...@gmail.com:
W dniu poniedziałek, 8 lipca 2013 16:44:20 UTC+1 użytkownik Christoph
Junghans napisał
upgrade to 1.3 as I am not an
administrator.
On Monday, July 8, 2013 10:26:41 PM UTC+1, Christoph Junghans wrote:
2013/7/8 s.neu...@gmail.com:
W dniu poniedziałek, 8 lipca 2013 18:00:32 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/8 s.neu...@gmail.com:
W dniu
for NAME.pot.in (in your case ACI-ACI.pot.in or
BAS-BAS.pot.in ) in step 0, so no need to add it to the file list.
Steven
W dniu środa, 10 lipca 2013 14:40:53 UTC+1 użytkownik Christoph Junghans
napisał:
2013/7/10 s.neu...@gmail.com:
W dniu wtorek, 9 lipca 2013 16:38:57 UTC+1
2013/7/10 s.neuman...@gmail.com:
W dniu środa, 10 lipca 2013 15:12:58 UTC+1 użytkownik Christoph Junghans
napisał:
2013/7/10 s.neu...@gmail.com:
Thank you! Shall remove distributions and replace in my mxl file target
into
name.pot.in ? Or shall I just add to the list of files in xml
the gromacs version it is compiled with
in the top somewhere.
Steven
On Wednesday, July 10, 2013 4:16:10 PM UTC+1, Christoph Junghans wrote:
2013/7/10 s.neu...@gmail.com:
I run the command to create the file ACI-ACI.in and I got the zero
potential
again. The same for two other files
2013/7/12 s.neuman...@gmail.com:
On Friday, July 12, 2013 8:39:24 AM UTC+1, s.neu...@gmail.com wrote:
On Friday, July 12, 2013 1:48:06 AM UTC+1, Christoph Junghans wrote:
2013/7/11 s.neu...@gmail.com:
Dear Users,
I am running IBI - My system involves 90 beads, protein chain. Each
which makes it so complicated.
Steven
And to be clear: My potentials goes o zero at large r.
What do you mean?
Steven
W dniu poniedziałek, 15 lipca 2013 17:44:46 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/15 s.neu...@gmail.com:
Votca is definitely wrong. If you take
are
15 potentials which makes it so complicated.
Steven
And to be clear: My potentials goes o zero at large r.
What do you mean?
Steven
W dniu poniedziałek, 15 lipca 2013 17:44:46 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/15 s.neu...@gmail.com:
Votca
2013/7/15 s.neuman...@gmail.com:
W dniu poniedziałek, 15 lipca 2013 17:44:46 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/15 s.neu...@gmail.com:
Votca is definitely wrong. If you take the example of maximum of my
ACI-ACI.dist.tgt the maximum corresponds to 65.555. The potential
W dniu poniedziałek, 15 lipca 2013 17:44:46 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/15 s.neu...@gmail.com:
Votca is definitely wrong. If you take the example of maximum of my
ACI-ACI.dist.tgt the maximum corresponds to 65.555. The potential at
this
point should be: W
://groups.google.com/group/votca.
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Web: http://www.compphys.de
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2013/7/22 s.neuman...@gmail.com:
On Friday, July 19, 2013 8:02:01 PM UTC+1, Christoph Junghans wrote:
2013/7/19 s.neu...@gmail.com:
Thank you for this.
I recalculated my distributions and make them a value between 0 and 1 at
large distances. If I submit then my own potential pot.in
at -35 kJ/mol, which is -14 K_bT.
Statistically it is very unlikely that reach any value more 3 k_bT
away for the min.
Christoph
Steven
W dniu poniedziałek, 22 lipca 2013 23:40:50 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/22 s.neu...@gmail.com:
On Friday, July 19, 2013 8:02
poniedziałek, 22 lipca 2013 23:40:50 UTC+1 użytkownik Christoph
Junghans napisał:
2013/7/22 s.neu...@gmail.com:
On Friday, July 19, 2013 8:02:01 PM UTC+1, Christoph Junghans wrote:
2013/7/19 s.neu...@gmail.com:
Thank you for this.
I recalculated my distributions and make them
2013/7/23 s.neuman...@gmail.com:
W dniu wtorek, 23 lipca 2013 16:24:25 UTC+1 użytkownik Christoph Junghans
napisał:
2013/7/23 s.neu...@gmail.com:
Another example which seems to be correct but wish to know, please see
attached. The derivative (last column) of function H(x) is zero while
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