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/CMakeError.log.
I have some ideas what could be the problem:
1.) Do you have pkg-config installed?
2
Sorry for so many posts, just experimenting, another update:
I can create one bond distribution at a time. So if I specify in the
mapping.xml and in commands to extract one bond at a time everything
works:) Just have to run csg_boltzmann twice to get my potentials.
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That's great. Thank you very much!
I guess I didn't pick it from the examples/manual.
On Aug 10, 11:02 am, Victor Rühle rue...@votca.org wrote:
Dear Valentina,
you have a little bug in your mapping. Youll have to define a sepaerate
bond section for each bond type:
cg_bonded
bond
Thank you for your reply.
I did turn it off, as error message suggested also.
V
On Aug 16, 10:39 pm, Christoph Junghans jungh...@votca.org wrote:
Hi Valentina,
this is really a bug, we did experienced it so far as it only happens
in some cases.
I fixed it in the code:
http
checkout the stable branch with 'hg update
stable' or add --dev option (disable this check with the --no-
branchcheck option)
I also tried putting --no-branchcheck or --dev but it didn't seem to
help.
Thank you very much for your help,
Valentina
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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
while
specify the right trajectory type in cg.inverse.gromacs.traj_type.
The default is xtc, but if you set nstxtcout in grompp.mdp to 0, the
xtc file is not created.
Cheers,
Christoph
2011/8/18 Valentina valentina_erast...@yahoo.co.uk:
Thank you very much for your quick replies
, 9:39 pm, Valentina valentina_erast...@yahoo.co.uk wrote:
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
to calculate autocorrelations.
-have a look at CMakeCache.txt to tweak other options related to fftw.
Cheers,
Christoph
2011/8/19 Valentina valentina_erast...@yahoo.co.uk:
Thank you:
[root@xena src]# more /opt/votca/src/tools/CMakeFiles/CMakeError.log
Determining if the function
Thank you very much, I did get GNU gsl and it worked (till next error
- posted into more relevant discussion).
Valentina
On Sep 5, 8:57 am, Christoph Junghans jungh...@votca.org wrote:
Hi Valentina,
the cblas thing is a bit misleading, it is only needed by libgsl, so
make sure you have GNU
Great! Thank you very much.
I managed to install it on the cluster, there was smth funny with pkg-
config indeed. (One more machine to go, but I think I know where the
problem lays now)
Valentina
On Sep 6, 3:25 pm, Christoph Junghans jungh...@votca.org wrote:
Hi Valentina,
after we had
Hello, I am getting same error as in his discussion (but I cannot
write on there)
http://groups.google.com/group/votca/browse_thread/thread/c814a046ebd31191/dcced561c1b51c60?lnk=gstq=Votca+1.2+released+#dcced561c1b51c60
Linking CXX executable linktest
libvotca_tools.so.2: undefined reference to
Ok I overcame this problem somehow:)
Need to specify paths make sure fftw is double precision (oops)
V
On Sep 22, 1:40 pm, Valentina valentina_erast...@yahoo.co.uk wrote:
Hello, I am getting same error as in his discussion (but I cannot
write on there)
http://groups.google.com/group/votca
#
#
#
###
Terminated
I will go and try removing my mpi update onto the settings file
meanwhile.
Is there something I am missing?
Many thanks,
Valentina
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To post
OK, update, it works without mpi part. I must have messed something up
there. Will go and try sorting it out.
On Sep 27, 3:57 pm, Valentina valentina_erast...@yahoo.co.uk wrote:
I have installed votca on a cluster. Then I have transfered my working
files from computer i previously used (single
Ooopsie, thank you very much!
On Sep 27, 4:06 pm, Victor Ruehle rue...@votca.org wrote:
Hey,
mpi
tasks8/tasks
cmdmpirun -np 8 /cmd
mpi
you forgot the / for the mpi closing tag. Last line should be /mpi
Best,
Victor
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Ok seems to work with just adding inverse.gromacs.mdrun.command added
and I removing inverse.mpi part (from above) completely.
:) V
On Sep 27, 4:26 pm, Valentina valentina_erast...@yahoo.co.uk wrote:
I am still stuck with mpi (i guess) I am getting this, what does it
mean? I guess i managed
/scriptdir
log_fileinverse.log/log_file
restart_filerestart_points.log/restart_file
/inverse
/cg
Thank you very much,
V
On Oct 3, 11:06 am, Victor Ruehle rue...@votca.org wrote:
Dear Valentina,
thanks for pointing it out. I tested the mapping and bonding stuff for
quite a few things
Hi Sacha, I had similar problem at first, just to realise after that
in my grompp.mdp, settings.xml and index.ndx I have not specified
correctly non-bonded groups correct names. Here is what I did to get
mines working, so mb good to double check yours are all fine too.
So tabulated bond and
Hi Marc,
Make sure all of paths are to correct places (ie 4.5.3) when
compiling. You may need to specify this paths in ./build.sh
-DGMX_INCLUDE_DIR=/usr/local/gromacs-4.5.3/include
-DGMX_LIBRARY=/usr/local/gromacs-4.5.3/lib
also mb make sure it's consistent here too: export PKG_CONFIG_PATH=/
mb find where is gromacs 4.5.5 is and make sure that
you manually specify paths correctly?
Sorry it wasn't much use.
V
On Oct 21, 11:13 pm, Marc Segovia marcsego...@gmail.com wrote:
Hi Valentina
Thanks by your reply, I try your suggestion, but the problem
persist.IMHO is about that when
Yes, you are absolutely right. I forgot there is meant to be some order.
Thank you!
On Tuesday, October 16, 2012 3:29:01 PM UTC+1, Christoph Junghans wrote:
2012/10/16 Valentina valentina...@yahoo.co.uk javascript::
Hello!
I am trying to install votca with --dev and getting
have a solution?
Many thanks,
V
On Aug 4, 3:03 pm, Christoph Junghans jungh...@votca.org wrote:
Hi Valentina,
it seems like you have compiled VOTCA without gromacs support.
Please check that again. tpr and xtc files need gromacs support.
Cheers,
Christoph
2011/8/4 Valentina Erastova
Hi, have you used scaling by by 1 /4 \pi r^2for bond and by 1/ sin (\theta)
for angle distribution?
I assume those are angles bonds.
Best,
V
On 12 Aug 2013, at 16:39, s.neuman...@gmail.com wrote:
Dear Users,
I run 7500 iterations of the protein with 5 different bead types so 15
is in NVT?
W dniu poniedziałek, 12 sierpnia 2013 17:02:36 UTC+1 użytkownik Valentina
Erastova napisał:
Hi, have you used scaling by by 1 /4 \pi r^2for bond and by 1/ sin (\theta)
for angle distribution?
I assume those are angles bonds.
Best,
V
On 12 Aug 2013, at 16:39
dniu wtorek, 13 sierpnia 2013 10:49:13 UTC+1 użytkownik Valentina Erastova
napisał:
Hi,
I am a little confused there.
You need to have a well equilibrated system before you CG. My way is to run
NPT, but make sure that the system is equilibrated and V is also constant.
When you start CG
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