I found a possible bug in the library file gmxtrajectoryreader.cc in
votca-csg/scr/csg/libcsg/modules/io.
There in lines 75 and in lines 132 it could be that m[i][j] =
_gmx_frame.box[i][j]; instead of m[i][j] = _gmx_frame.box[j][i]; is correct
and a possible index switch occured.
I am not sure
s, which is useful
> when using lammps.
>
> So in which cases do the xy and yx values get switched? A xtc to gro
> conversion or gro to gro?
>
> Cheers,
>
> Christoph
>
> 2015-07-03 9:51 GMT-06:00 Christoph Scherer >:
> > I found a possible bug in t
Mittwoch, 8. Juli 2015 10:43:59 UTC+2 schrieb Christoph Junghans:
>
>
> Am 07.07.2015 14:03 schrieb "Christoph Scherer" >:
> >
> > Hi Christoph,
> >
> > Thank You for the fast reply. I just noticed the switch in the xy to yx
> coordinates when I
My experience so far is that when parametrizing all interactions together
of course mor memory is needed (a linear system of equations is solved for
all degrees of freedom together). But if there is not enough memory,
csg_fmatch crashes with an error of bad_alloc in the output. So if that not
h
That is true,
the result is different, if You parametrize the interactions separately or
not. (If memory allows, all interactions should be parametrized together as
then the "optimal solution" is found for all spline coefficients of all
interactions with respect to all other interactions.)
I
Hi Rom,
maybe you can post the fmatch.xml file and the ouput of csg_fmatch? Did you
use the exact same votca version than before?
Best
Christoph
Am 12.09.2016 21:45 schrieb "Rom" :
> Hi all,
>
> I keep getting a segmentation fault when attempting to run csg_fmatch on
> my system.
> I have forc
>
> If there is not enough sampling, the number of frames is to small or the
> grid size is to fine, the csg_fmatch error will normally be":
an error occurred:
constrained_qrsolve_zero_column_in_matrix
Maybe it is a Gromacs error? (But for using csg_fmatch, the Gromacs run
should have been fi
I just checked again, and as far as I remember it is not a leftover from
the thermodynamic force integration, but I implemented it in terms of usind
it with csg_fmatch. It applies a smoothing function of the form y = y*cos(
pi*(x-x_switch)/(2*(x_end-x_switch)) ) to all table values between x_swi
Hi Shiyun,
my first Idea when reading the error message was, have you used a c++
compiler that is supporting the c++11 standard. Because, when adding
features for the 3body parametrization, I have explicitly used classes from
c++ 11.
Best
Christoph
Am Mittwoch, 24. Mai 2017 10:00:50 UTC+2
Actually you do not need the other table values. If you set the appropriate
parameters in the topol.top file (see the tutorials of ibi e.g.) it is
sufficient to have columns 6 and 7 with your full force and potential.
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Hello,
if you pull the VOTCA code from github, you in principle have access to all
older releases. (To see how to install votca, check out e.g. the
documentation on https://github.com/votca/csg/wiki/Installing.). To use an
older version, you should first create the appropriate folder and go int
Hi,
you can run csg_fmatch with the --no-map option. Then it will act on the
original Gromacs trajectory with the Gromacs Atom names. The question is what
exactly do you mean by pairwise force? csg_fmatch will give you the average
force between the specific atom pairs averaged over all! interac
Hi,
for mehr the Files look in principle ok. In case of the settings File of course
IT depends which forces you want to parametrize. To getan the firce between the
O and H Atoms, I would try force matching with the mapping file you sebt. Then
I would try to cases. One settings file with O-H non
Sorry, I am at holiday at the moment and only have my smartphone. Therefore all
the typos. In about two weeks, I can help you better.
Best Christoph
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Hi,
Sure. No problem.
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Hi, I am back now. Did you already resolve the problem?
Am Sonntag, 30. Juli 2017 20:45:31 UTC+2 schrieb Christoph Scherer:
>
> Hi,
>
> Sure. No problem.
>
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So what exactly have you done so far and where do you still hav problems?
Am Donnerstag, 17. August 2017 22:36:27 UTC+2 schrieb M. Chakraborty:
>
> Hello,
> No. I did not solve the problem yet.
>
> ~M. Chakraborty
>
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Hi,
I just read the message and looked into the files. In my opinion, the issue
is the same than above. The file bond-RB-RA.dist.new contains only 0s and
therefore dpot.pure_ibi has no valid entries. The setup looks okay to me. I
also rerun the gromacs simulation with the tabulated potentials p
Hi, I didn't see that your original trajectory was done with LAMMPS. Sorry.
So, you do not have to concert the energies then.
Best
Christoph
CHRISTINA-ANNA GATSIOU schrieb am Do., 25.
Apr. 2019, 17:07:
> I am just confused cause you suggested the conversion to kcal/mol even
> though my initial
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