Hey,
i also use csg_boltzmann, the tab command (dont forget tab set scale
bond / tab set scale angle for bond/angles). some of my examples (the
.pot files are the output of csg_boltzmann):
bonds:
cp ../../pot/AB_bond.pot .
sed -e '1,5d' -e 's/$/ i/' AB_bond.pot | tac | sed -e '1,4d' | tac >
AB.cut ; cut bad sampled regions at the boundaries
csg_call table smooth AB.cut AB.smooth
csg_resample --in AB.smooth --out AB.refined --grid 0::0.001:0.5
csg_call table extrapolate --function quadratic AB.refined AB.pot.cur
csg_call --ia-type bonded --ia-name AB --options ../convert.xml
convert_potential gromacs
angles:
cp ../../pot/ABC_angle.pot .
#sed -e '1,3d' -e 's/$/ i/' ABC_angle.pot | tac | sed -e '1,3d' | tac > ABC.cut
sed -e 's/$/ i/' ABC_angle.pot | tac | sed -e '1,2d' | tac > ABC.cut
csg_call table smooth ABC.cut ABC.smooth
csg_resample --in ABC.smooth --out ABC.refined --grid 0::0.001:3.141592654
csg_call table extrapolate --function quadratic --region left
ABC.refined ABC.refined
csg_call table extrapolate --function linear --region right
ABC.refined ABC.refined
awk '{print $1/3.141592654*180.0,$2}' ABC.refined > ABC.pot.cur
csg_call --ia-type angle --ia-name ABC --options ../convert.xml
convert_potential gromacs
convert.xml:
<cg>
<bonded>
<name>AB</name>
<inverse>
<gromacs>
<table>../tables/table_b0.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<name>BC</name>
<inverse>
<gromacs>
<table>../tables/table_b1.xvg</table>
</gromacs>
</inverse>
</bonded>
<angle>
<name>ABC</name>
<inverse>
<gromacs>
<table>../tables/table_a0.xvg</table>
</gromacs>
</inverse>
</angle>
<inverse>
<gromacs>
<table_end>3.0</table_end>
<table_bins>0.002</table_bins>
<pot_max>1000000</pot_max>
</gromacs>
</inverse>
</cg>
Diheral i currently don't have tabulated one (fitted functional form
in my case), but should be similar.
Best,
Victor
2011/6/27 chemistry <[email protected]>:
> In this case I have to multiply x value (rad) on (180/3.14) and
> afterwords I can use this distribution function for getting the
> potential and if it's not zero just simply shift it to zero?
>
> On Jun 27, 3:20 pm, Christoph Junghans <[email protected]> wrote:
>> You can shift the minimum to zero, it will not change the simulation
>> result (except for a energy offset).
>> In VOTCA 1.2 the shifting is done automatically if you are using
>> 'csg_call convert_potential gromacs'
>>
>> Notice that for angles csg_boltzmann calculates everything in rad,
>> while gromacs (xvg files) wants degrees, so double check the scale of
>> the x values again.
>>
>> Cheers,
>>
>> Christoph
>>
>> 2011/6/27 chemistry <[email protected]>:
>>
>> > I calculated the potential with awk and with csg_boltzmann. It gives
>> > the same shape of the curves but in the case when I used awk the
>> > minimum of the potential has negative value. Should I shift the
>> > minimum of the potential to zero? Does csg_boltzmann do it
>> > automatically?
>>
>> > Thanks a lot in advance,
>> > Sergio
>>
>> > On Jun 26, 4:42 pm, Christoph Junghans <[email protected]> wrote:
>> >> Hi Sergio,
>>
>> >> the potentials have to look similar around the minimum. The region
>> >> left and right are usually extrapolated and the exact form of the
>> >> extrapolation does not matter much as the appearance of these values
>> >> is exponentially suppressed (exp -E/k_bT).
>> >> Make sure that the area {U_min..U_min+k_b T} is correct.
>>
>> >> Technically what I do to obtain table_b1.xvg is:
>> >> -calculate the distribution with csg_stat / csg_boltzmann
>> >> -calculate the potential using awk
>> >> $ awk -v kbt=NUMBER '{print $1,($1>0)?-kbt*log($2/$1/$1):"nan"}'
>> >> bond.dist.new > bond.pot.new
>> >> -take a look at the potential and cut it down to the well-sampled region
>> >> -convert it to gromacs format (this was reworked in VOTCA 1.2, before
>> >> the extrapolation had to be done by hand)
>> >> $ csg_call --options bond.xml --ia-type bonded convert_potential
>> >> gromacs bond.pot.new2 table_b1.xvg
>> >> where bond.xml looks like this:
>> >> <cg>
>> >> <inverse>
>> >> <program>gromacs</program>
>> >> <gromacs>
>> >> <pot_max>1e8</pot_max>
>> >> <table_end>3</table_end>
>> >> <table_bins>0.002</table_bins>
>> >> </gromacs>
>> >> </inverse>
>> >> </cg>
>>
>> >> table.xvg is used to calculate the interactions for all pairs, which
>> >> do not appear in energygrp_table (in the mdp file).
>> >> If all pairs are covered by energygrp_table combinations you can use
>> >> any table, but I would use a table filled with zeros.
>> >> table.xvg can be useful in cases when you want to mix IBI tables with
>> >> a standard force field, then table.xvg should be the default 6-12 LJ
>> >> table ($GMXDATA/gromacs/top/table6-12.xvg)
>>
>> >> Cheers,
>>
>> >> Christoph
>>
>> >> 2011/6/26 chemistry <[email protected]>:
>>
>> >> > Thanks a lot for the previous advices!
>>
>> >> > I have one more question about table_*.xvg. Can you explain please how
>> >> > exactly did you create all tables for the propane which you used for
>> >> > the ibi-procedure (table.xvg, table_a1.xvg, table_b1.xvg). I did the
>> >> > post-processing of the potentials (bond and angle) and I've got the
>> >> > same shape for the potentials but much more higher value for the y-
>> >> > axis. The distribution functions and potentials for bond and angle are
>> >> > the same like in your presentation. Did I do something wrong or is it
>> >> > something else what I should know? And which role plays table.xvg in
>> >> > this case?
>>
>> >> > Thanks a lot in advance,
>> >> > Sergio.
>>
>> >> > On Jun 23, 11:34 am, Christoph Junghans <[email protected]> wrote:
>> >> >> Hi Sergio,
>>
>> >> >> 2011/6/22 chemistry <[email protected]>:> Thanks a lot for advice,
>> >> >> I checked all again and I found the mistake
>> >> >> > in my mappin.xml file. I fixed it and now it works well.
>> >> >> > Is it something important in the calculation of the rdf in the
>> >> >> > iterations for such a systems?
>>
>> >> >> Usually one don't want to consider pairs of beads, which interact via
>> >> >> a bonded potential, for the rdf.
>> >> >> The reason is that the rdf is used to calculate the non-bonded
>> >> >> interaction and so only the pairs which interact non-bonded should go
>> >> >> in the rdf.
>>
>> >> >> However in some cases it is useful to calculate the rdf with different
>> >> >> exclusions than the simulation was performed. (the
>> >> >> cg.inverse.gromacs.rdf.topol option in the xml setting file, see the
>> >> >> manual)
>>
>> >> >> Cheers,
>>
>> >> >> Christoph
>>
>> >> >> > Thanks a lot in advance.
>> >> >> > Sergio
>>
>> >> >> > On Jun 21, 6:02 pm, Victor Ruehle <[email protected]> wrote:
>> >> >> >> Hmm, are you sure that all the beads which should be excluded are
>> >> >> >> part of an angle definition? If yes, Votca should exclude them
>> >> >> >> automatically..
>>
>> >> >> >> I'm doing a very similar thing and it worked for me. Will check
>> >> >> >> tomorrow whether there might be a new bug.However, third or fourth
>> >> >> >> nearest neighbors should still be visible, there is no option so far
>> >> >> >> to exclude all beads in the molecule. I could add that if necessary.
>>
>> >> >> >> Please verify if the peaks you observe really correspond to second
>> >> >> >> nearest neighbors, and if yes whether you have this particular
>> >> >> >> angle
>> >> >> >> defined in the mapping. Also check csg_dump --excl
>>
>> >> >> >> 2011/6/21 chemistry <[email protected]>:
>>
>> >> >> >> > I'm trying to calculate the target rdf for polymer system with the
>> >> >> >> > "csg_stat" and also I'm interested to calculate the rdf in the
>> >> >> >> > iterations:
>>
>> >> >> >> > csg_stat --top topol.tpr --trj traj.xtc --options settings.xml
>> >> >> >> > --cg
>> >> >> >> > mapping.xml
>>
>> >> >> >> > I have P3HT system. Every monomer divided on the three beads.
>> >> >> >> > Thiophene ring represented the first bead and hexyl chain divided
>> >> >> >> > on
>> >> >> >> > the two beads - each bead include three carbon atoms.
>>
>> >> >> >> > in the settings.xml file I specified the types of the beads which
>> >> >> >> > are
>> >> >> >> > the same like in the mapping.xml:
>>
>> >> >> >> > .............
>> >> >> >> > <non-bonded>
>> >> >> >> > <!-- name of the interaction -->
>> >> >> >> > <name>P1-P1</name>
>> >> >> >> > <!-- types involved in this interaction -->
>> >> >> >> > <type1>A</type1>
>> >> >> >> > <type2>A</type2>
>> >> >> >> > <!-- dimension + grid spacing of tables for calculations -->
>> >> >> >> > <min>0</min>
>> >> >> >> > <max>1.36</max>
>> >> >> >> > <step>0.01</step>
>> >> >> >> > <inverse>
>> >> >> >> > <!-- target distribution (rdf), just give gromas rdf.xvg -->
>> >> >> >> > <target>P1-P1.dist.tgt</target>
>> >> >> >> > <!-- update cycles -->
>> >> >> >> > <do_potential>1 0 0</do_potential>
>> >> >> >> > <!-- additional post processing of dU before added to
>> >> >> >> > potential
>> >> >> >> > -->
>> >> >> >> > <post_update></post_update>
>> >> >> >> > <!-- additional post processing of U after dU added to
>> >> >> >> > potential
>> >> >> >> > -->
>> >> >> >> > <post_add></post_add>
>> >> >> >> > <!-- name of the table for gromacs run -->
>> >> >> >> > <gromacs>
>> >> >> >> > <table>table_P1_P1.xvg</table>
>> >> >> >> > </gromacs>
>> >> >> >> > </inverse>
>> >> >> >> > </non-bonded>
>> >> >> >> > ...............
>>
>> >> >> >> > ---mapping.xml---:
>>
>> >> >> >> > <cg_molecule>
>> >> >> >> > <name>P3HT</name>
>> >> >> >> > <ident>Protein_X</ident>
>> >> >> >> > <topology>
>> >> >> >> > <cg_beads>
>> >> >> >> > <cg_bead>
>> >> >> >> > <name>S1</name>
>> >> >> >> > <type>A</type>
>> >> >> >> > <symmetry>1</symmetry>
>> >> >> >> > <mapping>A</mapping>
>> >> >> >> > <beads> 1:BBB:S01 1:BBB:C01 1:BBB:C02 1:BBB:H01 1:BBB:C03
>> >> >> >> > 1:BBB:C04 1:BBB:H02 </beads>
>> >> >> >> > </cg_bead>
>> >> >> >> > ................
>>
>> >> >> >> > Also I specified all <bonds> and <angles> and <weights>. It works
>> >> >> >> > well, but the second nearest neighbor does not excluded from the
>> >> >> >> > rdf.
>> >> >> >> > Seems that the exclusion works just for the first nearest
>> >> >> >> > neighbor. Is
>> >> >> >> > it possible to exclude this interaction from the rdf?
>>
>> >> >> >> > On Jun 17, 11:11 am, Victor Rühle <[email protected]> wrote:
>> >> >> >> >> Hey,
>>
>> >> >> >> >> Can you please describe you problem in more details, what
>> >> >> >> >> exactly did
>> >> >> >> >> you try? Are you referring to calculating the target rdf, or the
>> >> >> >> >> rdf in
>> >> >> >> >> the iterations?
>>
>> >> >> >> >> We introduced proper exclusion handling in version 1.1, so it
>> >> >> >> >> should
>> >> >> >> >> work. You can check whether exclusions are read correctly by:
>>
>> >> >> >> >> csg_dump --top topol.tpr --excl
>>
>> >> >> >> >> or if you use csg_stat to calculate target rdf:
>>
>> >> >> >> >> csg_dump --top topol.tpr --cg mappin.xml --excl
>>
>> >> >> >> >> If you use g_rdf, you have to specify the topology -s topol.tpr
>> >> >> >> >> in
>> >> >> >> >> addition to an index file.
>>
>> >> >> >> >> A brief side-note:
>> >> >> >> >> Be aware, that for the reference rdf and that during the
>> >> >> >> >> iterations, the
>> >> >> >> >> exact identical normalization should be used (there is room for
>> >> >> >> >> some
>> >> >> >> >> discrepancy, however as far as i could see it's more problematic
>> >> >> >> >> for IMC
>> >> >> >> >> than for IBI). Therefore better use the same program for both
>> >> >> >> >> (csg_stat
>> >> >> >> >> to calculate reference). In version 1.2, which was released
>> >> >> >> >> yesterday,
>> >> >> >> >> we have adjusted the normalization to be identical to g_rdf in
>> >> >> >> >> gromacs 4.5.
>>
>> >> >> >> >> Victor
>>
>> >> >> >> >> On 06/17/2011 10:32 AM, chemistry wrote:
>>
>> >> >> >> >> > I have one addition question about the ibi procedure. I have a
>> >> >> >> >> > polymer
>> >> >> >> >> > chain and I'm doing ibi for non-bonded interactions. How can I
>> >> >> >> >> > exclude
>> >> >> >> >> > the bond part from the RDF? Because in my case I have all the
>> >> >> >> >> > same
>> >> >> >> >> > beads in the backbone chain of my polymer and when I'm
>> >> >> >> >> > calculating the
>> >> >> >> >> > RDF it does not correspond to the purely non-bond
>> >> >> >> >> > interactions. This
>> >> >> >> >> > RDF except the non-bonded part includes the bonded part.
>>
>> >> >> >> >> > Thanks a lot in advance.
>> >> >> >> >> > Sergio
>>
>> >> >> >> >> > On Jun 14, 2:59 pm, chemistry <[email protected]> wrote:
>> >> >> >> >> >> Thanks a lot for advice. Now ibi procedure works.
>>
>> >> >> >> >> >> On Jun 9, 8:31 pm, Victor Ruehle <[email protected]> wrote:
>>
>> >> >> >> >> >>> Hey,
>> >> >> >> >> >>> did you source your VOTCA installation?
>>
>> ...
>>
>> read more »
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To post to this group, send email to [email protected].
> To unsubscribe from this group, send email to
> [email protected].
> For more options, visit this group at
> http://groups.google.com/group/votca?hl=en.
>
>
--
You received this message because you are subscribed to the Google Groups
"votca" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/votca?hl=en.
