ght be doing wrong, or a potential fix? I'm also
> not getting perfect agreement to the potential of mean force (e.g.,
> -kTln(Pr))for the step001 angle and bond potentials either, but this might
> partially be due to the shifting you are doing.
>
> Thanks again for your help.
>
&g
fed in as $ARGV[0] into the perl script?
>>
>> Thanks.
>>
>> Josh
>
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n it,
> so think it overrides the previous block. Seems to be updating now.
Good that you found it, I have seen that problem before!
Christoph
>
> I will do a pull request later today after a bit more testing, but I think
> it's ok now.
>
> Thanks.
>
> Josh
>
>
>
2017-02-16 13:29 GMT-07:00 Sikandar Mashayak <symasha...@gmail.com>:
>
>
> On Thu, Feb 16, 2017 at 2:23 PM, Christoph Junghans <jungh...@votca.org>
> wrote:
>>
>> 2017-02-16 13:05 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>:
>> > Hi Christoph,
&g
n is to do 1 for all interaction, meaning do
pressure correction every step.
And adjust the scaling factor (i.e. XXX) to something smaller.
Christoph
>
> Thanks.
>
> Josh
>
> On Thursday, February 16, 2017 at 3:43:43 PM UTC-5, Christoph Junghans
> wrote:
>>
>> 2017-
. I've run each iteration up to 250,000
> MD steps so far.
I fixed the forces for bond now:
<https://github.com/votca/csg/commit/567a37802a748bf3a73345f39fb02d1a5903aabe>
Christoph
>
> Josh
>
>
>
> On Tue, Feb 14, 2017 at 12:44 AM, Christoph Junghans <jungh...@votca.org>
> wrote:
cribed to the Google Groups
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or this great tool!
> -Robert Elder
>
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of libgromacs in csg.
Cheers,
Christoph
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y has A-B.
Christoph
>
> On Monday, February 27, 2017 at 3:39:09 PM UTC-6, Christoph Junghans wrote:
>>
>> 2017-02-27 13:35 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>:
>> > Hi there,
>> > I had obtained bonded tabulated potentials for our study molecule using
&
oups.com.
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You received this message bec
o IBI on the bonded interaction, too? Or are they fixed?
Christoph
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
>
> On Wed, Aug 31, 2016 at 4:16 PM, Christoph Junghans <jungh...@votca.org>
> wrote:
>>
>> 2016-08-31 12:24 GMT-06:00 Chang Woon Jang <changw
too? Or are they fixed?
Christoph
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
>
>
> On Wed, Aug 31, 2016 at 5:21 PM, Christoph Junghans <jungh...@votca.org>
> wrote:
>>
>> 2016-08-31 14:51 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>
it https://groups.google.com/d/optout.
>
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2016-08-29 14:47 GMT-06:00 Christoph Junghans <jungh...@votca.org>:
> 2016-08-29 14:37 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
>> Dear Christoph,
>>
>>
>> What I have used is the following command with the options.xml file.
>>
>
le Groups
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ers.)
Seems to work for at least 10k steps.
Cheers,
Christoph
2016-08-29 20:52 GMT-06:00 Christoph Junghans <jungh...@votca.org>:
> 2016-08-29 15:19 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
>> Dear Christoph,
>>
>>Can I run ibi without dihedr
t; # ERROR:
> #
> # do_external: subscript
> #
> # /home/chang/PACKAGE/votca/share/votca/scripts/inverse/table_linearop.pl
> --on-x table_d1.xvg table_d1.pot.scale.Jdqcv 57.2957795 0 #
> # (from tags table linearop) failed
> #
> # Details can be found above
> #
> #
s?
Basically you look at the distributions and find the well-sampled region.
For angle, usually 0 to pi works ok, but for the bond it is more hand tuning.
Christoph
>
>
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Tue, Aug 30, 2016 at 2:04 PM, Christoph
Did you also change original bond and angle tables to gromacs format?
>>
>> If so, how do I determine the min and max values for bond and angle
>> tables?
>>
>>
>>
>> Thank you.
>>
>> Best regards,
>> Changwoon Jang
d, for
> pairs and tabulated bonds also see option -ddcheck
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Best regards,
> Changwoon
ly the non-bonded interactions are iterated.
Christoph
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Mon, Aug 29, 2016 at 4:30 PM, Christoph Junghans <jungh...@votca.org>
> wrote:
>>
>> 2016-08-29 13:32 GMT-06:00 Chang Woon Jang <changwo
is group at https://groups.google.com/group/votca.
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delphia, PA 19104
>
> Voice: (662) 617-2267
> E-mail: cj...@drexel.edu
>
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lation crash.
Christoph
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Wed, Aug 31, 2016 at 11:05 AM, Christoph Junghans <jungh...@votca.org>
> wrote:
>>
>> 2016-08-31 8:43 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
>> &
n Kumar Choudhury
>> Post Doctoral Fellow
>> Clemson University
>> South Carolina
>> USA
>>
>> "All work and no play makes Jack a dull boy...”
>
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ributions?
>
What do you mean by shifting?
Christoph
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> For more options,
entials with the MARTINI
force-field. Mixing structure-based and free-energy-based potential gives
unpredictable results. To check you could study a single molecule in vacuum
and compare your bonded interactions.
Christoph
>
> On Friday, September 9, 2016 at 8:26:07 PM UTC+5:
Best regards.
> Nancy
>
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e.
However, you still have the same options as IBI is having, e.g. update
order and scaling factor.
Christoph
>
> --Vitalie
>
> On Tuesday, October 4, 2016 at 5:19:42 PM UTC+2, Christoph Junghans wrote:
>>
>>
>> See Fig. 8 of http://dx.doi.org/10.1063/1.4947253 fo
to reinstall them since i installed cmake3.6.2
>>>
>>> -- The following REQUIRED packages have not been found:
>>>
>>>
>>> * Boost (required version >= 1.39.0)
>>>
>>>
>>> -- Configuring incomplete, errors occurred!
>>>
>>>
>
you are subscribed to the Google Groups
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2 (include)
> cmake_install.cmake:32 (include)
>
> How do I keep my prefix=src/votca? I do no find the error here.
You could use e.g. $HOME/votca
Christoph
>
> Thanks for your help,
> Nancy
>
>
>
>
>
>
>
> On Wednesday, 5 October 2016 18:06:07 UTC+2, Christo
2016-10-04 8:37 GMT-06:00 Devon Dillon <devondillon...@gmail.com>:
> will this reduce the functionality of my votca program?
No, you will just have no manpages!
Christoph
>
>
> On Tuesday, October 4, 2016 at 9:11:15 AM UTC-5, Christoph Junghans wrote:
>>
>> 2016-10-
d_cibi_correction.sh#L69>
>> I would implement that in a similar fashion as
>>
>> <https://github.com/votca/csg/blob/master/share/scripts/inverse/table_switch_border.pl>
>> which put a cos function over a table.
>>
>> Christoph
>>
>>
>> --
>
> -- Looking for C++ include algorithm
>
> -- Looking for C++ include algorithm - found
>
> -- Looking for sqrt in m
>
> -- Looking for sqrt in m - found
>
> -- Configuring incomplete, errors occurred!
>
> See also
> "/Users/Dillon/ProgramBuilds/VOTCA
2016-10-05 9:46 GMT-06:00 Christoph Junghans <jungh...@votca.org>:
> 2016-10-05 1:29 GMT-06:00 Vitalie Botan <vitalie.bo...@gmail.com>:
>> Does it have any parameters to play with, like integral cutoff, fudge factor
>> etc.? Or in the current version it is all fi
t; of distributions look smoothly.
If the *target* rdf haven't change for a bigger system, you are fine.
Christoph
>
> I will try the rest options.
>
> Thank you again!
> Best regards,
> Zidan
>
>
>
> On Monday, 19 September 2016 18:15:06 UTC+2, Christoph Junghans wrote:
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&
will NOT fix any bugs in Votca 1.3.X
anymore, so we encourage everyone to update and use the new version.
Cheers,
Christoph
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2017-01-12 21:44 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>:
> Thank you for the help.
Does it work now?
>
> On Thursday, January 12, 2017 at 9:34:39 PM UTC-6, Christoph Junghans wrote:
>>
>> 2017-01-12 10:10 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>
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the settings.xml, a postadd or
postupd wrapper needs to be added.
Javi, what did you had in mind?
Christoph
>
>
> Am Mittwoch, 12. April 2017 18:36:24 UTC+2 schrieb Christoph Junghans:
>>
>> 2017-04-12 8:00 GMT-06:00 Javier Ramos <jrd...@gmail.com>:
>> > Dear a
elf as nobody has done something similar, yet.
Plus, the work might not worth it due to the fact that at most you can
save a factor 2 (in comparison to running your analysis tool twice).
Christoph
>
> Thanks,
> Alireza
>
> On Thursday, April 13, 2017 at 8:43:01 AM UTC-5, Christoph J
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gt; ALC
>>
>> 0
>> 1.5
>> 0.01
>>
>>
>> CC-ALC.dist.tgt
>>
>> 1 0 0
>>
>>
>>
>> convergence
>>
>>
>> table_CC_ALC.xvg
>&g
in
> potential_extrapolate.sh.
Does this work for you: <https://github.com/votca/csg/pull/203> ?
>
> Thanks.
>
> Josh
>
> On Friday, March 10, 2017 at 12:43:01 PM UTC-5, Christoph Junghans wrote:
>>
>> 2017-03-10 0:05 GMT-07:00 Joshua Moore <jdm...@ncsu.edu
ading to issues in the simulation,
>> at least I think this is the reason. Please see attached.
>>
>> Do we need to add back in the end calculation as you were mentioning?
>> Maybe that was needed.
>>
>> Thanks.
>>
>> Josh
>>
>>
>>
>>
&g
isit this group at https://groups.google.com/group/votca.
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> smoothing step which again drops most of the points and appears to be the
>> major issue here.
>>
>> I think the dihedral issue might be a general issue in VOTCA and not
>> necessarily a problem with interfacing with LAMMPS?
>>
>>
>> Thank
DH1.xvg
>
>
>
>
> What could be problem? And thank you for the support.
Looks good so far!
Is there a "table_CC_DH1.xvg" in your step_001? Can you attach your inverse.log?
Christoph
>
> On Tuesday, February 28, 2017 at 4:14:47 PM UTC-6, Christoph Junghans wrote
is assigned number 4.
>>>
>>> I greatly appreciate any further help you can provide.
>>>
>>> Best,
>>> Torsten
>>>
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advance.
>
> Best regards,
> JIng
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2017-08-14 3:05 GMT-06:00 <sufigueroa0...@gmail.com>:
> Hi Christoph, thanks a lot,
> the installation had actually problems. The administrator of the cluster
> reinstalled and now it is working :)
> S.
Thanks for the update.
>
> On Friday, 11 August 2017 20:35:57 UTC+2,
On Aug 17, 2017 03:14, "J. Li" <jing...@rug.nl> wrote:
Thanks for your reply, Christoph,
Distribution function which has to be looked at is that of the target
atomistic simulation?
Yes!
Christoph
Thanks again.
Best,
Jing
On Wednesday, August 16, 2017 at 2:42:05 PM UTC+2, Ch
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9-13, 2017
in Stuttgart, Germany
Please check the web page for details:
<https://www.cecam.org/workshop-1523.html>
and don't hesitate to contact us if you have any questions.
Cheers,
Christoph
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2017-06-08 16:24 GMT-06:00 Christoph Junghans <jungh...@votca.org>:
> 2017-06-08 15:56 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>:
>> Hello,
>>
>> I was following the hexane hybrid tutorial and there [exclusions] were
>> included in the topology
2017-06-20 11:08 GMT-06:00 Christoph Junghans <jungh...@votca.org>:
> 2017-06-19 19:15 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>:
>> Dear Christoph,
>>
>> The OpenMPI problem has been solved by adding the full path of gfortran to
>> f77 and fc in the
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Application::Exec(int, char**) ()
> from /software/votca/b2/lib/libvotca_tools.so.5
> #9 0x0041a1d3 in main ()
> (gdb) quit
>
>
> Thanks.
>
> ~M. Chakraborty
>
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ched the entire on screen printed
>> > information and the cmake error file. The file names with "_noBoostPath"
>> > correspond to the first building command (no boost path is specified)
>> > while
>> > the file names with "_withBoostPath" correspond
stoph
>
> On Wednesday, 24 May 2017 17:08:13 UTC-4, Christoph Junghans wrote:
>>
>> 2017-05-24 14:11 GMT-06:00 M. Chakraborty <maghe...@gmail.com>:
>> > I am trying to use the tabulated potential (for non-bonded interactions)
>> > obtained from force-matchin
o recompile boost in another directory using gcc-6.1
I recently added votca to spack, so you might have a chance to install
it that way:
<https://github.com/votca/csg/wiki/Installing#spack>
Christoph
>
> For the third one: my system is Centos, it seems there is not votca instal
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"v
for the
trajectory will need to be calculated using minimum image convention
anyhow, so having some atom sticking out won't hurt.
Christoph
>
> On Friday, 2 June 2017 18:23:05 UTC-4, Christoph Junghans wrote:
>>
>> 2017-06-02 13:16 GMT-06:00 M. Chakraborty <maghe...@gmail.com>:
>&
to votca@googlegroups.com.
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"vo
; Your further help is greatly appreciated.
> Best regards,
> Shiyun
>
>
> 在 2017年5月28日星期日 UTC+8上午5:24:27，Christoph Junghans写道：
>>
>> 2017-05-26 21:02 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>:
>> > Dear Christoph,
>> >
>> > Thanks a l
mpty so I did not attached it.
If it fails building OpenMPI, that is really more a question for the
spack mailing list:
<https://groups.google.com/d/forum/spack>
or its issue tracker:
<https://github.com/LLNL/spack/issues>
Christoph
>
> THanks a lot.
> Shiyun
>
>
ard.
>
> For the third one: my system is Centos, it seems there is not votca install.
Centos7 now has a votca package:
<https://github.com/votca/csg/wiki/Installing#centos-7>
Christoph
>
> Best Regards,
> Shiyun
>
>
> 在 2017年5月27日星期六 UTC+8上午12:22:32，Christoph Junghans写道：
if Votca-1.4 is enough for you, do:
<https://github.com/votca/csg/wiki/Installing#centos-7>
and install only votca-ctp and moo on top of it using build.sh.
Christoph
>
> Thanks a lot
> Best regards,
> Shiyun
>
>
>
> 在 2017年6月13日星期二 UTC+8下午10:29:26，Christoph Jun
in DCMAKE_PREFIX_PATH, it indeed works
> without appearing the warnings.
> The bug of spack has been reported.
Thanks, can you also report the openmpi issue on Centos7.
Thanks,
Christoph
>
> Thanks again for the help!
>
> With best regards,
> Shiyun
>
> 在 2017年6月15日星期四 UTC+8下午11:2
oglegroups.com.
> To post to this group, send email to votca@googlegroups.com.
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Christoph Junghans
Web: http://www.compphys.de
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;votca" group.
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> For more options, vi
et the large amount of lines that "gmx dump"
> prints out, so to check that its output is correct:
> - you could check that with the previously attached .tpr
> - I could follow some instructions on how to use "gmx dump".
>
>
> Best,
> Albert
>
> On
/lammps-17Nov16/src/lmp_mpi
in the block here, see Section 10.4 (pg 55) of
<http://votca.github.io/doxygen/manual.pdf>
Christoph
>
> spce.in
>
> topol.xml
>
> traj.dump
>
>
>
> Could you please point out what is the mist
p, send email to votca@googlegroups.com.
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"votca
Albert,
2017-10-13 3:50 GMT-06:00 Albert Solernou <a.soler...@gmail.com>:
> Hi Cristoph,
> I am afraid your answer does not fully address the point. See the comments
> inlined, please.
>
> On Tuesday, October 3, 2017 at 8:34:46 PM UTC+1, Christoph Junghans wrote:
>>
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