Hi,
2014-12-28 4:17 GMT-07:00 Francesca Stanzione <[email protected]>:
> Hi Christoph,
> unfortunately I tried to update the votca version but it is not working. I
> have the same error. I changed the spacing in the settings.xml to a
> reasonable one (0.002) and I also changed the spacing in the
> ABB-angle.dist.tgt.
> Any additional suggestion?
Ok, I looked at the original problem again and there seems to be a
rounding problem with step/gromacs.table_bins=0.0005.
Basically numbers get rounded in each potential conversion step and
hence after a while one gets the "Illegal division by zero" as two x
values become too similar. I still have not found out, where exactly
it goes wrong and add a warning.
In addition, Gromacs internally uses a spacing of 0.002 (single
precision) or 0.0005 (double precision), so 0.0005 would only make
sense with double precision Gromacs. But double precision isn't really
needed for coarse-grained simulation with thermostats. Have you tried
using gromacs.table_bins=0.002 ?
With gromacs.table_bins=0.002 and the following patch, I got your
table running in hexane/ibi_bonded example.
diff -r a4ed014029f5 hexane/ibi_bonded/settings.xml
--- a/hexane/ibi_bonded/settings.xml Fri Oct 10 03:40:35 2014 -0600
+++ b/hexane/ibi_bonded/settings.xml Sun Dec 28 11:54:25 2014 -0700
@@ -16,12 +16,12 @@
<bonded>
<!-- name of the interaction -->
<name>angle</name>
- <min>1.7</min>
+ <min>0.9</min>
<max>3.1</max>
- <step>0.02</step>
+ <step>0.002</step>
<inverse>
<!-- target distribution -->
- <target>angle.dist.tgt</target>
+ <target>ABB-angle.dist.tgt</target>
<gromacs>
<table>table_a1.xvg</table>
</gromacs>
But anyhow, step=0.002 is still 1100 bins which need to be filling
with statistics, which is a lot, you should aim for something like
0.02.
Like I said in my last email, you might have better chances generating
a custom initial guess for your angle potential.
Christoph
>
> Thank you,
> Francesca
>
>
> 2014-12-19 13:24 GMT-05:00 Christoph Junghans <[email protected]>:
>>
>> 2014-12-18 15:36 GMT-07:00 Francesca Stanzione
>> <[email protected]>:
>> > Dear all,
>> > I am experiencing a problem to convert the angle potential in a
>> > table.xvg
>> > I have a polymer chain composed by 7 beads with two beadstypes A and B.
>> > The
>> > polymer sequence is: A1-B1-B2-B3-B4-B5-A2. I have 2 bondtypes (AB and
>> > BB)
>> > and two angletypes (ABB and BBB).
>> > I obtained the dist.tgt. When I try to run the IBI it works for the
>> > bonds
>> > but not for the angles. Because I supposed I was doing something wrong I
>> > tried the hexane and propane tutorials to see if something was wrong
>> > with my
>> > angles or my settings.xml and I am not able to obtained the tabulated
>> > potential for angle neither for them.
>> > This is the error I get:
>> > ERROR:
>> > #
>> > # do_external: subscript
>> > #
>> > # /home/software/votca/share/votca/scripts/inverse/table_to_xvg.pl --max
>> > 1000000 --type angle ABB-angle.pot.shift.YkwA2 table_a0.xvg #
>> > # (from tags convert_potential xvg) failed
>> > #
>> > # For details see the logfile inverse.log
>> >
>> >
>> > THIS IS the DETAILS FROM THE inverse.log
>> >
>> > or_all: run 'do_external convert_potential gromacs
>> > $(csg_get_interaction_property name).pot.cur
>> > $(csg_get_interaction_property
>> > inverse.gromacs.table)' for interaction named 'ABB-angle'
>> > Running subscript 'potential_to_gromacs.sh ABB-angle.pot.cur
>> > table_a0.xvg'
>> > (from tags convert_potential gromacs) dir
>> > /home/software/votca/share/votca/scripts/inverse
>> > Convert ABB-angle.pot.cur to table_a0.xvg
>> > Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\)
>> > .*/\1/p'
>> > Running critical command 'mktemp ABB-angle.pot.scale.XXXXX'
>> > Running subscript 'table_linearop.pl --on-x ABB-angle.pot.cur
>> > ABB-angle.pot.scale.dHEeQ 57.2957795 0' (from tags table linearop) dir
>> > /home/software/votca/share/votca/scripts/inverse
>> > table_linearop.pl: ABB-angle.pot.cur to ABB-angle.pot.scale.dHEeQ with
>> > x' =
>> > 57.2957795*x + 0
>> > Running critical command 'mktemp ABB-angle.pot.smooth.XXXXX'
>> > Running critical command 'csg_resample --in ABB-angle.pot.scale.dHEeQ
>> > --out
>> > ABB-angle.pot.smooth.bZWVq --grid 0:0.0286479:180'
>> > Running critical command 'mktemp ABB-angle.pot.extrapol.XXXXX'
>> > Running subscript 'potential_extrapolate.sh --type angle
>> > ABB-angle.pot.smooth.bZWVq ABB-angle.pot.extrapol.3ThKw' (from tags
>> > potential extrapolate) dir
>> > /home/software/votca/share/votca/scripts/inverse
>> > Extrapolate ABB-angle.pot.smooth.bZWVq to ABB-angle.pot.extrapol.3ThKw
>> > Running subscript 'table_extrapolate.pl --function linear --avgpoints 3
>> > --region leftright ABB-angle.pot.smooth.bZWVq
>> > ABB-angle.pot.extrapol.3ThKw'
>> > (from tags table extrapolate) dir
>> > /home/software/votca/share/votca/scripts/inverse
>> > table_extrapolate.pl: extrapolating the left using linear with gradient
>> > -8.60697674418617
>> > table_extrapolate.pl: extrapolating the right using linear with gradient
>> > -0.0167414651162821
>> > Running critical command 'mktemp ABB-angle.pot.interpol.XXXXX'
>> > Running critical command 'csg_resample --in ABB-angle.pot.extrapol.3ThKw
>> > --out ABB-angle.pot.interpol.j2iBK --grid 0:0.0005:180 --comment Created
>> > on
>> > Thu Dec 18 16:38:36 EST 2014 by fstanzio@silicon
>> > called from potential_to_gromacs.sh, version 1.3-dev hgid: 4fce95a62b88
>> > settings file:
>> > /home/Documents/bigger_box/reaction/ibi_cou_user/settings.xml
>> > working directory:
>> > /home/Documents/bigger_box/reaction/ibi_cou_user/step_001
>> > Comments from
>> >
>> > /home/Documents/bigger_box/reaction/ibi_cou_user/step_001/ABB-angle.pot.cur:\nCreated
>> > on Thu Dec 18 16:38:30 EST 2014 by fstanzio@silicon
>> > called from prepare_generic_single.sh, version 1.3-dev hgid:
>> > 4fce95a62b88
>> > settings file:
>> > /home/Documents/bigger_box/reaction/ibi_cou_user/settings.xml
>> > working directory:
>> > /home/Documents/bigger_box/reaction/ibi_cou_user/step_000'
>> > Running critical command 'mktemp ABB-angle.pot.shift.XXXXX'
>> > Running subscript 'potential_shift.pl --type angle
>> > ABB-angle.pot.interpol.j2iBK ABB-angle.pot.shift.YkwA2' (from tags
>> > potential
>> > shift) dir /home/software/votca/share/votca/scripts/inverse
>> > Running subscript 'table_to_xvg.pl --max 1000000 --type angle
>> > ABB-angle.pot.shift.YkwA2 table_a0.xvg' (from tags convert_potential
>> > xvg)
>> > dir /home/software/votca/share/votca/scripts/inverse
>> > Illegal division by zero at
>> >
>> > /home/fstanzio/software/votca/share/votca/scripts/inverse/table_to_xvg.pl
>> > line 96.
>> >
>> > Checking the xxx.pot.shift file I have "o" on the last 5 values, I tried
>> > to
>> > resample, to change the --grid to 179.5 (last value with "i") but
>> > nothing is
>> > working..
>> >
>> > I have the version 1.3-dev.
>> >
>> > I am sending you in addition the ABB-angle.dist.tgt and the settings.xml
>> > files.
>> > Can you please help me to understand what is the problem and why I am
>> > not
>> > able to have a table_angle?
>> Ok, it looks like ABB-angle.dist.tgt gets converted to
>> ABB-angle.pot.cur in step_000 and the conversion from
>> ABB-angle.pot.cur to
>> table_a0.xvg.
>>
>> However, with the latest version of VOTCA 1.3-dev (changeset:
>> 1e124eb53c82) I wasn't able to reproduce this problem, so please as
>> 0th step re-install VOTCA and see if the problem persists.
>> (<https://code.google.com/p/votca/wiki/Installing#Development_Version>)
>>
>> Independently, after looking at your files, I have a couple of issues:
>> 1.) a spacing of 0.02 in ABB-angle.dist.tgt might be a bit to fine,
>> when looking at the curve around 2.35, it very rough. IBI will never
>> be able to fit that. You will have to smooth the target distribution
>> first.
>> 2.) a spacing of 0.0005 for ABB-angle in settings.xml is by far too
>> fine. You will have to run really really long cg simulation in each
>> iteration to fill the 4400 (=2.2/0.0005) bins of that interaction with
>> statistic.
>> Remember that the stepping for each interaction doesn't have to be the
>> same as table_bins in gromacs block.
>>
>> Cheers,
>>
>> Christoph
>>
>>
>>
>> >
>> >
>> > Thank you,
>> > Francesca
>> >
>> > --
>> > 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
>> > an
>> > email to [email protected].
>> > To post to this group, send email to [email protected].
>> > Visit this group at http://groups.google.com/group/votca.
>> > For more options, visit https://groups.google.com/d/optout.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>> --
>> You received this message because you are subscribed to a topic in the
>> Google Groups "votca" group.
>> To unsubscribe from this topic, visit
>> https://groups.google.com/d/topic/votca/wcSWx0n900s/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> [email protected].
>> To post to this group, send email to [email protected].
>> Visit this group at http://groups.google.com/group/votca.
>> For more options, visit https://groups.google.com/d/optout.
>
> --
> 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 an
> email to [email protected].
> To post to this group, send email to [email protected].
> Visit this group at http://groups.google.com/group/votca.
> For more options, visit https://groups.google.com/d/optout.
--
Christoph Junghans
Web: http://www.compphys.de
--
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 an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at http://groups.google.com/group/votca.
For more options, visit https://groups.google.com/d/optout.
