Hi Christoph (or other VOTCA developers),
I tired to ask my question on the forum :
https://groups.google.com/forum/#!forum/votca
But after pressing the "Post" button my message failed to appear amongst
the topics.
I have to retype it now because the text has been lost.
Well, I have been using
Dear VOTCA developers,
I have had VOTCA installed for a couple of years, both locally (on a
desktop) and on a Beowulf cluster.
I am using it with both Gromacs and DL_POLY. Everything worked nicely until
recently.
Now when I am trying to use csg_stat like this:
csg_stat --top .dlpf --trj
Hi again,
Sorry, it was my bad input... hard to spot.
The error was caused by a missing bead name in one of the
subsections in the mapping file
(so there were only three instead of four beads specified).
At least, we know now that this sort of omission in the mapping xml-file
results in such
Hi Christoph & Sikandar,
It's been a while since I asked the question below...
On Monday, July 23, 2018 at 7:51:14 PM UTC+1, Andrey Brukhno wrote:
>
>
> >>> Actually, I am a bit confused not seeing re.traj tag for atomistic
>> >>> trajectory. I thought RE iteration requires recalculating CG
Wow, nobody can answer this straightaway? - I wonder: does this mean that
no non-associate of the VOTCA team ever used RE method for their actual
problem (i.e. not a tutorial case)?
Anyway, may I ask those on the team now: in what relation VOTCA's B-spline
definition is with the corresponding
Well, to reduce the burden on the developers' answering (probably obvious
for them) questions, here is what I discovered by simply plotting the
CG-CG.param.init file from the tutorial in csg-tutorials/spce/re/
The CG-CG.param.init file appears to contain the -RT\ln(g_{target}(r)) data
sampled
>
> Best,
> Sikandar
>
> On Thu, Jul 19, 2018 at 6:13 PM Christoph Junghans > wrote:
>
>>
>>
>> On Thu, Jul 19, 2018 at 18:15 'Andrey Brukhno' via votca <
>> vo...@googlegroups.com > wrote:
>>
>>> Hello,
>>>
>>> I
Hello,
I managed to run the RE iteration for a system with 10 non-bonded
potentials (types).. well, the first iteration anyway, where it terminated
after about an hour of running csg_reupdate with the following error:
*Hessian NOT a positive definite! *
This can be a result of poor initial
On Thursday, July 19, 2018 at 7:57:57 PM UTC+1, Christoph Junghans wrote:
>
> On Thu, Jul 19, 2018 at 10:44 AM, 'Andrey Brukhno' via votca
> > wrote:
> > I get:
> >
> > ... ...
> > Total number of parameters to optimize: 333
> > an error occur
Ok, I will give it a try on my home PC.
Andrey
On Thursday, July 19, 2018 at 8:19:03 PM UTC+1, Christoph Junghans wrote:
>
> On Thu, Jul 19, 2018 at 10:57 AM, 'Andrey Brukhno' via votca
> > wrote:
> >
> >
> > On Thursday, July 19, 2018 at 4:48:14 PM UTC+
Well, I tried to follow your instructions in this thread for "stable"
branch.
Andrey
On Fri, 20 Jul 2018 22:41 Christoph Junghans, wrote:
> On Fri, Jul 20, 2018 at 3:11 PM, 'Andrey Brukhno' via votca
> wrote:
> > The problem is, I remembered this option for the old bu
Andrey
On Sat, Jul 21, 2018 at 1:48 AM, Christoph Junghans
wrote:
>
>
> On Fri, Jul 20, 2018, 16:49 'Andrey Brukhno' via votca <
> votca@googlegroups.com> wrote:
>
>> Well, I tried to follow your instructions in this thread for "stable"
>> branch.
>
Hello,
The last time I was installing the CSG package in my Ubuntu (up-to-date
2014 LTS) I got this error from cmake: eigen3 not found, with a suggestion
to provide the path to it. I then downloaded the library from their
website, installed it and added its include directory to both my $PATH
Hello,
In an attempt to compare some data obtained with IBI to RE, I am trying to
start a relative entropy iteration for the same system. However, I do not
know how to generate the initial parameters (aka CG-CG.param.init file) for
my system (which would comprise 10 different interaction
On Mon, Jul 23, 2018 at 5:07 PM, Christoph Junghans
wrote:
> On Mon, Jul 23, 2018 at 9:22 AM, 'Andrey Brukhno' via votca
> wrote:
> >
> >
> > On Friday, July 20, 2018 at 2:08:19 AM UTC+1, Christoph Junghans wrote:
> >>
> >>
> >>
> >&
On Monday, July 23, 2018 at 8:18:39 PM UTC+1, Andrey Brukhno wrote:
>
> On Monday, July 23, 2018 at 3:17:49 PM UTC+1, Christoph Junghans wrote:
>>
>> On Mon, Jul 23, 2018 at 7:41 AM, 'Andrey Brukhno' via votca
>> wrote:
>> > In this case, it's not an error
On Monday, July 23, 2018 at 3:17:49 PM UTC+1, Christoph Junghans wrote:
>
> On Mon, Jul 23, 2018 at 7:41 AM, 'Andrey Brukhno' via votca
> > wrote:
> > In this case, it's not an error message which is lost ;) Why does it go
> to
> > stderr at all?
>
On Monday, July 23, 2018 at 3:17:49 PM UTC+1, Christoph Junghans wrote:
>
> On Mon, Jul 23, 2018 at 7:41 AM, 'Andrey Brukhno' via votca
> > wrote:
> > In this case, it's not an error message which is lost ;) Why does it go
> to
> > stderr at all?
>
On Friday, July 20, 2018 at 2:08:19 AM UTC+1, Christoph Junghans wrote:
>
>
>
> On Thu, Jul 19, 2018 at 17:26 'Andrey Brukhno' via votca <
> vo...@googlegroups.com > wrote:
>
>>
>>
>> On Thursday, July 19, 2018 at 7:57:57 PM UTC+1, Christoph Junghans w
thing.
>
> --
> Sikandar
>
> On Mon, Jul 23, 2018 at 9:11 AM Christoph Junghans
> wrote:
>
>> On Mon, Jul 23, 2018 at 9:28 AM, 'Andrey Brukhno' via votca
>> wrote:
>> > Any comment on this "shift" issue?
>> > I tried to find the relevant scri
On Tue, Jul 24, 2018 at 1:34 AM, Christoph Junghans
wrote:
> On Mon, Jul 23, 2018 at 5:26 PM, 'Andrey Brukhno' via votca
> wrote:
> >
> >
> > On Monday, July 23, 2018 at 8:18:39 PM UTC+1, Andrey Brukhno wrote:
> >>
> >> On Monday, July 23, 2018 at
It seems that mapping files are only used for IBI.
Andrey
On Tue, Jul 24, 2018 at 1:31 AM, Christoph Junghans
wrote:
> On Mon, Jul 23, 2018 at 4:14 PM, 'Andrey Brukhno' via votca
> wrote:
> > On Monday, July 23, 2018 at 3:17:49 PM UTC+1, Christoph Junghans wrote:
> >>
Ok, good to know! - Not that I could follow the workflow by the link though.
Andrey
On Sat, Jul 21, 2018 at 7:33 PM, Christoph Junghans
wrote:
>
>
> On Thu, Jul 19, 2018 at 09:47 Christoph Junghans
> wrote:
>
>> On Thu, Jul 19, 2018 at 9:33 AM, 'Andrey Brukhno
Hello,
I encountered a very strange (looks like legacy) issue with v1.4.1.
In my earlier IBI iterations (with v1.3) I normally used special
topol-rdf.tpr which was different from normal CG simulation topol.tpr by
not including the intra-molecular pairs in the RDF stats (done by
csg_stat). I
dfs and its errors for interaction NH-NH
On Sun, Jul 22, 2018 at 1:26 PM, Christoph Junghans
wrote:
> On Sat, Jul 21, 2018 at 9:01 PM, 'Andrey Brukhno' via votca
> wrote:
> > Hello,
> >
> > I encountered a very strange (looks like legacy) issue with v1.4.1.
>
On Sat, Jul 21, 2018 at 7:42 PM, Christoph Junghans
wrote:
>
>
> On Fri, Jul 20, 2018 at 18:59 'Andrey Brukhno' via votca <
> votca@googlegroups.com> wrote:
>
>> By now I have installed SQLITE3, compiled latest version of Gromacs and
>> currently installing VOTCA
On Mon, Jul 23, 2018 at 2:22 AM, Christoph Junghans
wrote:
> On Sun, Jul 22, 2018 at 1:27 PM, 'Andrey Brukhno' via votca
> wrote:
> > Thanks for your reply Christoph.
> >
> > I did check it, but inverse.log does not contain sufficient info, see the
> > extract belo
On Mon, Jul 23, 2018 at 1:17 PM, Christoph Junghans
wrote:
> On Mon, Jul 23, 2018 at 2:39 AM, 'Andrey Brukhno' via votca
> wrote:
> >
> > On Mon, Jul 23, 2018 at 2:22 AM, Christoph Junghans
> > wrote:
> >>
> >> On Sun, Jul 22, 2018 at 1:27
rukhno' via votca
> > wrote:
> >
> > On Mon, Jul 23, 2018 at 2:22 AM, Christoph Junghans >
> > wrote:
> >>
> >> On Sun, Jul 22, 2018 at 1:27 PM, 'Andrey Brukhno' via votca
> >> > wrote:
> >> > Thanks for your reply
On Mon, Jul 23, 2018 at 1:50 PM, Christoph Junghans
wrote:
> On Mon, Jul 23, 2018 at 6:46 AM, 'Andrey Brukhno' via votca
> wrote:
> > Sorry, I forgot - below is the output of `grep critical inverse.log' for
> one
> > iteration:
> >
> > Running critical co
echo"# Creating new logfile (-errors) #"
echo -e "##\n\n"
msg "For a more verbose log see: ${CSGLOG##*/} (or csg_inverse.log)"
fi
This worked before and did not affect the workflow.
Andrey
On Mon, Jul 23, 2018 at
> Calculating rdfs with csg_stat using 4 tasks
> >> >> >> > Calculating average rdfs and its errors for interaction TCH-TCH
> >> >> >> > rdf calculation is already done
> >> >> >> > Calculating average rdfs and its e
On Monday, July 23, 2018 at 2:33:44 PM UTC+1, Christoph Junghans wrote:
>
> On Mon, Jul 23, 2018 at 7:28 AM, 'Andrey Brukhno' via votca
> > wrote:
> > Christoph,
> >
> > I think I figured why there is no log msg for critical csg_stat in
> > calc_rdfgen
On Mon, Jul 23, 2018 at 1:46 PM, Christoph Junghans
wrote:
> On Mon, Jul 23, 2018 at 6:39 AM, 'Andrey Brukhno' via votca
> wrote:
> > On Mon, Jul 23, 2018 at 1:17 PM, Christoph Junghans
> > wrote:
> >>
> >> On Mon, Jul 23, 2018 at 2:39 AM, 'A
ing the target
> RDFs, i.e., c_i = -kTlog(g(r_i)). I have found this approach of
> initializing knot values work well in my RE coarse-graining experiments.
>
> Best,
> Sikandar
>
> On Wed, Jul 18, 2018 at 4:42 PM 'Andrey Brukhno' via votca <
> vo...@googlegroups.com >
Hello again,
By now, that the simulation for one iteration has finished (successfully),
I got a similar error during the analysis:
# ERROR:
On Thursday, July 19, 2018 at 4:48:14 PM UTC+1, Christoph Junghans wrote:
>
> >>
> >> > We recently fixed an issue in the Eigen3 detection:
> >> >
> >> >
> https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
>
> >> > which includes:
> >> >
> >> >
>
Hi Christoph,
On Thursday, July 19, 2018 at 4:01:48 PM UTC+1, Christoph Junghans wrote:
>
> On Thu, Jul 19, 2018 at 8:56 AM, 'Andrey Brukhno' via votca
> > wrote:
> > Hello,
> >
> > Anyone encountered this error?
> >
> > $ csg_reupdate --gentab
On Thursday, July 19, 2018 at 3:27:52 PM UTC+1, Christoph Junghans wrote:
>
> On Wed, Jul 18, 2018 at 12:20 PM, Christoph Junghans > wrote:
> > On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca
> > > wrote:
> >> Hello,
> >>
> >
Hello,
Anyone encountered this error?
$ csg_reupdate --gentable true --param-in-ext param.new --options
./settings.xml -v
an error occurred:
property not found: re.function
while the settings.xml file does contain the correctly formatted subsection
for each potential, like below
cbspl
Thanks Christoph!
That was helpful - I restarted iteration now.
On Thursday, July 19, 2018 at 7:57:57 PM UTC+1, Christoph Junghans wrote:
>
> On Thu, Jul 19, 2018 at 10:44 AM, 'Andrey Brukhno' via votca
> > wrote:
> > Hello again,
> >
> > By now, that the si
On Tuesday, July 24, 2018 at 12:48:40 PM UTC+1, Christoph Junghans wrote:
>
> On Tue, Jul 24, 2018 at 2:31 AM, 'Andrey Brukhno' via votca
> > wrote:
> >
> >
> > On Tue, Jul 24, 2018 at 1:34 AM, Christoph Junghans >
> > wrote:
> >>
> >
votca <
votca@googlegroups.com> wrote:
>
> On Tuesday, July 24, 2018 at 12:48:40 PM UTC+1, Christoph Junghans wrote:
>>
>> On Tue, Jul 24, 2018 at 2:31 AM, 'Andrey Brukhno' via votca
>> wrote:
>> >
>> >
>> > On Tue, Jul 24, 2018 at 1:34 AM, C
Hello,
Upon a successful installation of the VOTCA's development (master) branch I
get this error:
~/votca-dev/bin/csg_map
/home/andrey/votca-dev/bin/csg_map: error while loading shared libraries:
libvotca_csg.so.5: cannot open shared object file: No such file or directory
I tried to
the hood - ?).
Anyway, what is the cmake option to switch it off (I could not find it)?
Thanks
Andrey
On Saturday, September 8, 2018 at 6:01:02 PM UTC+1, Christoph Junghans
wrote:
>
> On Sat, Sep 8, 2018, 09:43 'Andrey Brukhno' via votca <
> vo...@googlegroups.com > wrote:
&g
ptember 8, 2018 at 6:42:03 PM UTC+1, Christoph Junghans
> wrote:
>>
>>
>>
>> On Sat, Sep 8, 2018 at 11:24 'Andrey Brukhno' via votca <
>> vo...@googlegroups.com> wrote:
>>
>>> The question is, what is the significance of this library (libhdf5)? -
Hi Christoph, thanks for your response.
On Friday, September 7, 2018 at 7:05:28 PM UTC+1, Christoph Junghans wrote:
>
> On Fri, Sep 7, 2018 at 11:03 AM 'Andrey Brukhno' via votca
> > wrote:
> >
> > Hello,
> >
> > Upon a successful installation of the VOTC
On Saturday, September 8, 2018 at 6:42:03 PM UTC+1, Christoph Junghans
wrote:
>
>
>
> On Sat, Sep 8, 2018 at 11:24 'Andrey Brukhno' via votca <
> vo...@googlegroups.com > wrote:
>
>> The question is, what is the significance of this library (libhdf5)? -
On Sat, Sep 8, 2018 at 8:08 PM Christoph Junghans
wrote:
>
> On Sat, Sep 8, 2018 at 12:52 'Andrey Brukhno' via votca <
> votca@googlegroups.com> wrote:
>
>>
>> On Saturday, September 8, 2018 at 7:40:43 PM UTC+1, Christoph Junghans
>> wrote:
>>>
n Saturday, September 8, 2018 at 4:05:08 PM UTC+1, Andrey Brukhno wrote:
>
> Hi Christoph, thanks for your response.
>
> On Friday, September 7, 2018 at 7:05:28 PM UTC+1, Christoph Junghans wrote:
>>
>> On Fri, Sep 7, 2018 at 11:03 AM 'Andrey Brukhno' via votca
>> wr
On Saturday, September 8, 2018 at 7:40:43 PM UTC+1, Christoph Junghans
wrote:
>
>
> On Sat, Sep 8, 2018 at 11:58 'Andrey Brukhno' via votca <
> vo...@googlegroups.com > wrote:
>
>>
>> On Saturday, September 8, 2018 at 6:42:03 PM UTC+1, Christoph Jun
. 3.1 from
> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131754 .
>
> Let me know if I missed anything.
>
> --
> Sikandar
>
> On Mon, Jul 23, 2018 at 9:11 AM Christoph Junghans > wrote:
>
>> On Mon, Jul 23, 2018 at 9:28 AM, 'Andrey Brukhno' via votca
>
s there any room for improvement in my preparation procedure?
Thanks
Andrey
> --
> Sikandar
>
>
>
> On Tue, Nov 20, 2018 at 3:28 AM 'Andrey Brukhno' via votca <
> vo...@googlegroups.com > wrote:
>
>> Hi Sikandar,
>>
>> Sorry for the delay. Attached is th
_CG1.xvg
---
On Friday, November 16, 2018 at 6:49:21 PM UTC, sikandar wrote:
>
> Hi Andrey,
>
> Could you please send me the raw data of your plots?
>
> Thanks,
> Sikandar
>
> On Tue, Nov 13, 2018 at 4:32 PM 'Andrey Brukhno' via votca <
> vo...@googlegroups.com >
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