2013/7/8 :
>
>
> W dniu poniedziałek, 8 lipca 2013 14:39:49 UTC+1 użytkownik Christoph
> Junghans napisał:
>>
>> 2013/7/8 :
>> > Dear Users,
>> >
>> > I am trying to run IBI. I have 5 type of beads: POL, NON, GLY, ACI, BAS
>> &
2013/7/8 :
>
>
> W dniu poniedziałek, 8 lipca 2013 16:44:20 UTC+1 użytkownik Christoph
> Junghans napisał:
>>
>> 2013/7/8 :
>> >
>> >
>> > W dniu poniedziałek, 8 lipca 2013 14:39:49 UTC+1 użytkownik Christoph
>> > Junghans napisał:
>
2013/7/8 :
>
>
> W dniu poniedziałek, 8 lipca 2013 18:00:32 UTC+1 użytkownik Christoph
> Junghans napisał:
>>
>> 2013/7/8 :
>> >
>> >
>> > W dniu poniedziałek, 8 lipca 2013 16:44:20 UTC+1 użytkownik Christoph
>> > Junghans nap
atomistic
bond/angle distribution. (see <http://dx.doi.org/10.1021/ct900369w>
for details)
> 在 2013年7月8日星期一UTC+8下午12时45分52秒，Christoph Junghans写道：
>>
>> 2013/7/7 郭志成 :
>> > Dear Christoph,
>> >
>> > Thanks for your help. It is working now. There is another q
gt; 4.48 0
>4.5 0
> 4.52 0
> 4.54 0
> 4.56 0
> 4.58 0
>4.6 0
> 4.62 0
> 4.64 0
> 4.66 0
> 4.68
2013 10:26:41 PM UTC+1, Christoph Junghans wrote:
>>
>> 2013/7/8 :
>> >
>> >
>> > W dniu poniedziałek, 8 lipca 2013 18:00:32 UTC+1 użytkownik Christoph
>> > Junghans napisał:
>> >>
>> >> 2013/7/8 :
>> >> >
e maximum of potential and it still
>> provides me with zero potentials... I cannot 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 :
>>> >
0
>> 3.74 0
>> 3.76 0
>> 3.78 0
>>3.8 0
>> 3.82 0
>> 3.84 0
>> 3.86 0
>> 3.88 0
>>3.9 0
>> 3.92
2013/7/10 :
>
>
> W dniu wtorek, 9 lipca 2013 16:38:57 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/7/9 :
>> > So the script prepare_generic_single.sh prepares empty potential.
>> > Please,
>> > see attached files
>> I save BA
ME.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 :
>> >
>> >
>> >
wtorek, 9 lipca 2013 16:38:57 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/7/9 :
>> > So the script prepare_generic_single.sh prepares empty potential.
>> > Please,
>> > see attached files
>> I save BAS-BAS.dist.tgt as BAS-BAS.dist.new
2013/7/10 :
>
>
> W dniu środa, 10 lipca 2013 15:12:58 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/7/10 :
>> > Thank you! Shall remove distributions and replace in my mxl file target
>> > into
>> > name.pot.in ? Or shall I just a
/Dist2Pot/sett
> ings.xml
> working directory:
> /home/ps/ps-fs2/jkm210/Polyglycine/CHANDLER/IBI_NON/Dist2Pot'
> Running subscript 'dpot_shift_nb.pl ACI-ACI.pot.new.smooth.385
> ACI-ACI.pot.new'(from tags pot shift_nonbonded)
>
>
>
> W dniu wtor
cannot change
> anything in both Votca or Gromacs as I am not an admin on the clsuter. Can I
> manually compile it somehow?
See:
<https://code.google.com/p/votca/wiki/Installing#From_Source>
"csg_stat --help" should show the gromacs version it is compiled with
in the top
up.
> To unsubscribe from this group and stop receiving emails from it, send an
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2013/7/12 :
>
>
> 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 :
>>> > Dear Users,
>>> >
>>>> Steven
>>>>
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "votca" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>&
e
>> 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
>&g
tentials goes to 0 which is correct.
I meant, which potential you are referring to?
The potential of main force U=- k_B*Tlog(g(r)), which VOTCA uses as an
initial guess, doesn't got to 0, it goes to infinity:
U(g(r)->0)=-log(g(r)->0) -> inf
>
> Steven
>
> W dniu poniedział
2013/7/15 :
>
>
> W dniu poniedziałek, 15 lipca 2013 17:44:46 UTC+1 użytkownik Christoph
> Junghans napisał:
>>
>> 2013/7/15 :
>> > Votca is definitely wrong. If you take the example of maximum of my
>> > ACI-ACI.dist.tgt the maximum corresponds to 65.
t; > In this case I guess I need thousands of iterations... The system input
>> > are
>> > 15 potentials which makes it so complicated.
>> >
>> > Steven
>> >
>> > W dniu poniedziałek, 15 lipca 2013 17:44:46 UTC+1 użytkownik Christoph
>>
hard to implement!
For IBI that would also make no difference as all normalization
factors drop out in the ratio g(r)/g_target(r) used in the update.
Christoph
>
> Steven
>
> W dniu wtorek, 16 lipca 2013 23:17:05 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2
t change the physics, so why are you so bother
about it? You could just to do IBI and shift the finial outcome once
it is converged.
Christoph
>
> Steven
>
> W dniu środa, 17 lipca 2013 17:43:51 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/7/17 :
>
send email to votca@googlegroups.com.
> Visit this group at http://groups.google.com/group/votca.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
--
Christoph Junghans
Web: http://www.compphys.de
--
You received this message because you are subscribed
2013/7/22 :
>
>
> On Friday, July 19, 2013 8:02:01 PM UTC+1, Christoph Junghans wrote:
>>
>> 2013/7/19 :
>> > Thank you for this.
>> > I recalculated my distributions and make them a value between 0 and 1 at
>> > large distances. If I submit t
lier
1.2 versions!
Also you potential has a minimum 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 napis
ve 4 potentials like
>> this out of 15...
>>
>> Steven
>>
>> W dniu poniedziałek, 22 lipca 2013 23:40:50 UTC+1 użytkownik Christoph
>> Junghans napisał:
>>>
>>> 2013/7/22 :
>>> >
>>> >
>>> > On Friday, July 1
2013/7/23 :
>
>
> W dniu wtorek, 23 lipca 2013 16:24:25 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/7/23 :
>> > Another example which seems to be correct but wish to know, please see
>> > attached. The derivative (last column) of function H
2013/7/24 :
>
>
> W dniu wtorek, 23 lipca 2013 20:05:45 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/7/23 :
>> >
>> >
>> > W dniu wtorek, 23 lipca 2013 16:24:25 UTC+1 użytkownik Christoph
>> > Junghans
>> > napisa
an shift your
potential by 1mio kJ/mol the thermodynamics will still be the same.
>
> Steven
>
>
>
> W dniu wtorek, 23 lipca 2013 20:05:45 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/7/23 :
>> >
>> >
>> > W dniu w
c.cc?repo=csg&name=stable#383>
>
>>
>>
>>
>> W dniu wtorek, 23 lipca 2013 20:05:45 UTC+1 użytkownik Christoph Junghans
>> napisał:
>>>
>>> 2013/7/23 :
>>> >
>>> >
>>> > W dniu wtorek, 23 lipca 2013 16:24:25 UT
in your xml file
- create a file csg_table with the following line
rdf gromacs my_rdf.sh
- get the default rdf calculation script:
$ csg_call --show rdf gromacs
- same it under the name my_rdf.sh
- modify my_rdf.sh
>
> Steven
>
>
> On Wednesday, July 24, 2013 5:22:01 PM UTC+1, Chris
2013/7/25 :
>
>
> On Wednesday, July 24, 2013 8:56:13 PM UTC+1, Christoph Junghans wrote:
>>
>> 2013/7/24 :
>> > My apologies, I am sorry for this but been fighting a long time with
>> > this.
>> >
>> > I wish I could use bonds as you ment
2013/7/25 :
>
>
> On Thursday, July 25, 2013 1:33:10 PM UTC+1, s.neu...@gmail.com wrote:
>>
>>
>>
>> On Wednesday, July 24, 2013 8:56:13 PM UTC+1, Christoph Junghans wrote:
>>>
>>> 2013/7/24 :
>>> > My apologies, I am sorry for th
a" group.
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> For more options, vi
ggest something please?
>
> Steven
>
>
>
>
>
> On Thursday, July 25, 2013 3:55:08 PM UTC+1, Christoph Junghans wrote:
>>
>> 2013/7/25 :
>> > And how g_rdf tool of gromacs will know which groups to use from
>> > index.ndx ?
>> That was one of t
this group at http://groups.google.com/group/votca.
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>
>
--
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Web: http://www.compphys.de
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rom it, send an
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--
Christoph Jungha
ld.
> collect2: error: ld returned 1 exit status
> make[2]: *** [src/libtools/linktest] Error 1
> make[1]: *** [src/libtools/CMakeFiles/linktest.dir/all] Error 2
> make: *** [all] Error 2
>
> Cannot understand the error. Hope some one can helo me out.
>
> Chandan
>
>
ature of the both the potentials should be same, but it is not so.
> Can someone point out what am I missing?
>
> Chandan
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Sun, Jul 28, 2013 at 3:07 AM, Christoph Junghans
> wrote:
>>
&
-e "${grp1}\n${grp2}" | critical ${g_rdf} -b ${begin} -n
"$index" -bin ${binsize} -o ${name}.dist.new.xvg -s "$tpr" -f
"${traj}" ${opts}
fi
Or replace the multi_g_rdf call with the normal g_rdf call for below.
>
> Thank you for your help!
5' failed #
>
> --12 could not be convert to a number
>
> Would you advise?
Change it back to what it was or change it to -9.
>
> Steven
>
>
> On Wednesday, July 31, 2013 4:29:16 PM UTC+1, Christoph Junghans wrote:
>>
>> 2013/7/31 :
>> > H
To unsubscribe from this group and stop receiving emails from it, send an
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DSOME_OPTION tools csg csg-manual
>
> Chandan
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Sat, Aug 3, 2013 at 11:03 PM, Christoph Junghans
> wrote:
>>
>> 2013/8/3 Chandan Choudhury :
>> > Dear votca users,
>> >
>
" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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> For more options, visit https://
gt
>
> 0 1 0
>
> convergence
>
>
> 1
> dist
>
>
>
>
>
> table_D_E.xvg
>
>
>
>
>
>
> E-E
>
ect.
Can you run the exact same csg_stat command as in csg_inverse? And
look at the result?
Find it with
$ grep csg_stat inverse.log
Christoph
>
> Chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
> --
> You received this message because you
m.
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>
>
--
Christoph Junghans
Web: http://www.compphys.de
--
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"votca" g
,
Christoph
PS: The school is generously supported the SimTech Cluster of Excellence and
the "Sonderforschungsbereich 716" of Stuttgart University.
--
Christoph Junghans
Web: http://www.compphys.de
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"vo
to the Google
>>>>> Groups "votca" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to votca+un...@googlegroups.com.
>>>>> To post to this group, send email to vo...@googlegr
2013/8/13 :
>
>
> W dniu wtorek, 13 sierpnia 2013 14:54:16 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/8/13 :
>> > Or is there any command which will tell csg_stat to get rid of PBC so
>> > that
>> > cell dimension will not have i
group.
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> For more options, visit ht
2013/8/13 :
>
>
> W dniu wtorek, 13 sierpnia 2013 16:08:49 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/8/13 :
>> >
>> >
>> > W dniu wtorek, 13 sierpnia 2013 14:54:16 UTC+1 użytkownik Christoph
>> > Junghans
>> &
2013/8/13 Christoph Junghans :
> 2013/8/13 Chandan Choudhury :
>>
>> Dear users,
>>
>> I am using votca version 1.3-dev for cg simulation.
>> At step_001, after the simulation by gromacs, csg_stat runs and it computes
>> the distributions (reads the setting.x
butions fo all the
>> bond distributions. Infact plots are overlapping for BC, CD and BE (when
>> compared with csg_stat).
>> I donot understand why only these to bonds are behaving in a different
>> way. I have attached the output of AB and DB bonds. AB contains -nan-.
&
2013/8/14 :
>
>
> W dniu wtorek, 13 sierpnia 2013 17:37:21 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/8/13 :
>> >
>> >
>> > W dniu wtorek, 13 sierpnia 2013 16:08:49 UTC+1 użytkownik Christoph
>> > Junghans
>>
2013/8/14 Chandan Choudhury :
>
> On Wed, Aug 14, 2013 at 7:39 PM, Christoph Junghans
> wrote:
>>
>> 2013/8/14 Chandan Choudhury :
>> >
>> > Thanks for fixing the bug. I made the changes in the source code and
>> > re-installed votca (1.3-dev).
r...@googlegroups.com.
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>
>
--
Christoph Junghans
Web: http://www.compphys.de
--
You received
o not needed. I just want to
>>>> convert my resampled and extrapolated dihedral to gromacs xvg:
>>>>
>>>> csg_call convert_potential xvg 19dihedralRES table_d19.xvg --type bond
>>>>
>>>> ERROR: table_to_xvg.pl: table for type non-bonded should
2013/8/15 Chandan Choudhury :
> On Thu, Aug 15, 2013 at 2:17 AM, Christoph Junghans
> wrote:
>>
>> 2013/8/14 Chandan Choudhury :
>> > Dear users,
>> >
>> > Is it possible just to iterate the bonded part (IBI, 1.3-dev). As I see
>>
;
> --
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2013/8/15 Chandan Choudhury :
>
> On Thu, Aug 15, 2013 at 10:48 PM, Christoph Junghans
> wrote:
>>
>> 2013/8/15 Chandan Choudhury :
>> > Dear votca users,
>> >
>> > The atomisitc trajectory produces a distribution of AB bond in the
>> > ra
n)+
extrapolation).
> Steven
>
> W dniu piątek, 16 sierpnia 2013 01:21:55 UTC+1 użytkownik Christoph Junghans
> napisał:
>>
>> 2013/8/15 Chandan Choudhury :
>> >
>> > On Thu, Aug 15, 2013 at 10:48 PM, Christoph Junghans
>> > wrote:
>> >>
&
om it, send an
> email to votca+unsubscr...@googlegroups.com.
> To post to this group, send email to votca@googlegroups.com.
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Web: http:/
re options, visit https://groups.google.com/groups/opt_out.
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eric_single.sh
edit my_post_update_generic.sh and remove shift from the for loop.
$ echo "post_update_single ibi my_post_update_generic_single.sh" >> csg_table
Good luck,
Christoph
>
> Steven
>
> W dniu czwartek, 22 sierpnia 2013 16:30:07 UTC+1 użytkownik Christop
2013/8/22 Chandan Choudhury :
>
>
> On Thu, Aug 22, 2013 at 8:46 PM, Christoph Junghans
> wrote:
>>
>> 2013/8/22 Chandan Choudhury :
>> > Dear votca users,
>> >
>> > I am stucked in some basic work flow of CG.
>> >
>> >
LAMMPS is now fully supported for IBI and IMC in VOTCA 1.3-dev!
Please have a look at:
<https://code.google.com/p/votca/source/browse/?repo=csg-tutorials#hg%2Fspce%2Fibi_lammps>
Cheers,
Christoph
2012/8/27 Christoph Junghans :
> 2012/8/27 karthik kumar :
>> Non-bonded potentia
2013/8/16 Christoph Junghans :
> 2013/8/16 :
>> I also have a question regarding bonded parameters using IBI. The initial
>> guess of those distributions should be an outcome from g_angle -dihedral
>> -dist or csg_boltzmann? They do differ quite significantly. Which tool VOT
legroups.com.
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You received this message
2013/8/29 Chandan Choudhury :
>
> On Thu, Aug 29, 2013 at 10:14 PM, Christoph Junghans
> wrote:
>>
>> 2013/8/29 Chandan Choudhury :
>> > Dear votca users,
>> >
>> > I have an angle distribution of beads, such that it peaks ~2.85 rad (163
>>
send an
> email to votca+unsubscr...@googlegroups.com.
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Web: http://www.compphys.de
DIA
>
>
> On Fri, Aug 30, 2013 at 10:08 AM, Chandan Choudhury
> wrote:
>>
>>
>>
>> On Thu, Aug 29, 2013 at 10:42 PM, Christoph Junghans
>> wrote:
>>>
>>> 2013/8/29 Chandan Choudhury :
>>> >
>>> > On Thu,
pot should have been created by csg_inverse in the directory step_001.
I have no problem running it:
$ csg_stat --help | grep version
csg_stat, version 1.3-dev hgid: cd57ac56f7d9 (compiled Sep 6 2013, 13:33:55)
votca_tools, version 1.3-dev hgid: 32b71329d1bf (compiled Sep 6 2013, 13:33:31)
$
###
>>
>> It needs a CG_CG.pot file. However, I dont know where this file is. Do I
>> need to copy from somewhere?
>>
>> Scott Sides
>> NREL
>
> --
> You received this message because you are subscribed to the Google Groups
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&
>> run 2500
>> ###
>>
>> It needs a CG_CG.pot file. However, I dont know where this file is. Do I
>> need to copy from somewhere?
>>
>> Scott Sides
>> NREL
>
> --
> You rece
I
>> need to copy from somewhere?
>>
>> Scott Sides
>> NREL
>
> --
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yle table linear 1000
>> >> pair_coeff 1 1 CG_CG.pot VOTCA 0.9
>> >>
>> >> timestep0.001
>> >> fix 1 all nve
>> >> fix 2 all langevin 2.49 2.49 0.2 545454
>> >>
>> >> dump
use you are subscribed to the Google Groups
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are not iterated.
>
> Chandan
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Fri, Sep 13, 2013 at 10:00 PM, Chandan Choudhury
> wrote:
>>
>>
>>
>> On Fri, Sep 13, 2013 at 9:21 PM, Christoph Junghans
>> wrote:
>>
.
>
>
> Chandan
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Sat, Sep 14, 2013 at 11:33 AM, Chandan Choudhury
> wrote:
>>
>>
>> On Sat, Sep 14, 2013 at 1:15 AM, Christoph Junghans
>> wrote:
>>&g
2013/9/14 Chandan Choudhury :
>
> On Sat, Sep 14, 2013 at 1:15 AM, Christoph Junghans
> wrote:
>>
>> 2013/9/13 Chandan Choudhury :
>> >
>> > Dear Christoph,
>> >
>> > I am attaching the bonded distribution of BC bond and the corresp
group/votca.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
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2013/10/1 Chandan Choudhury :
> On Tue, Oct 1, 2013 at 2:13 AM, Christoph Junghans
> wrote:
>>
>>
>> The trajectory is missing, just send a conf.gro. One frame will be
>> enough to check for the error.
>
>
> I have attached conf.gro
>>
>&
2013/10/1 Chandan Choudhury :
>
>
> On Tue, Oct 1, 2013 at 8:34 PM, Christoph Junghans
> wrote:
>>
>> There is a typo in your settings.xml, type2=C instead of D.
>> Anyhow after changing that I did:
>
> Thanks. It worked for me now.
>>
>> $
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an kumar Choudhury
> NCL, Pune
> INDIA
>
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t;> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>
>
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Christoph Junghans
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t; You received this message because you are subscribed to the Google Groups
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> Visit thi
sting on this topic). In short, a mpi version
of libgmx just pulls in more dependencies!
Christoph
>
> gmake[1]: *** [cmTryCompileExec3300959071] Error 1
>
> gmake[1]: Leaving directory
> `/gpfs/home/lsd001/votca_csg/src/csg/CMakeFiles/CMakeTmp'
>
> gmake: *** [cmTryCompi
2013/11/17 Zhicheng :
> Hi Christoph:
> Adding /usr/lib/libpthread.so to GROMACS_DEP_LIBRARY, however, I find the
> same error mentioned above . Does it need more dependencies?
Can you post the end of the new CMakeEtror.log again?
>
> 在 2013年11月16日星期六UTC+8上午12时28分01秒，Chris
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