Hey, Victor!
With table_b1.xvg and table_a1.xvg from your tutorial simulation for
propane works well.
I'd tried to process the potentials for propane myself and after when
I started the simulations I've got the same mistake like for my
system:
"Fatal error:
A tabulated bond interaction table number 1 is out of the table range:
r 3.157974, between table indices 3157 and 3158, table length 501"
Seems that I have some problem with creating the tables_*.xvg
Can you please check the way of post-processing of the potentials.
At the beginning I had the same shape of the potential like in your
case (I've got it with csg_boltzmann from all-atom MD simulation of
propane at T=200 K):
bond:
sed -e '1,5d' -e 's/$/ i/' AB.pot | tac | sed -e '1,4d' | tac > AB.cut
csg_call table smooth AB.cut AB.smooth
csg_resample --in AB.smooth --out AB.refined --grid 0::0.001:0.5
csg_call table extrapolate --function quadratic AB.refined AB.pot.cur
csg_call --options table.xml convert_potential xvg --type bonded
AB.pot.cur table_b1.xvg
where table.xml:
<cg>
<inverse>
<gromacs>
<pot_max>1e8</pot_max>
<table_end>0.5</table_end>
<table_bins>0.002</table_bins>
</gromacs>
</inverse>
</cg>
angle:
sed -e 's/$/ i/' ABA_angle.pot | tac | sed -e '1,2d' | tac > ABA.cut
awk '{print $1/3.141592654*180.0,$2,$3,$4}' ABA.cut > ABA.new.cut
csg_call table smooth ABA.new.cut ABA.smooth
csg_resample --in ABA.smooth --out ABA.refined --grid 0::0.05:180
csg_call table extrapolate --function quadratic ABA.refined
ABA.pot.cur
csg_call --options table.xml convert_potential xvg --type bonded
ABA.pot.cur table_a1.xvg
where table.xml:
<cg>
<inverse>
<gromacs>
<pot_max>1e8</pot_max>
<table_end>180</table_end>
<table_bins>0.05</table_bins>
</gromacs>
</inverse>
</cg>
In both cases the potentials look similar around the minimum, but
afterwords they are totally different. I wanted to get the same
table_*.xvg like in your example.
Yours respectfully,
Sergio
On Jul 1, 11:34 am, Victor Ruehle <[email protected]> wrote:
> Be aware, if you have a bug in your coarse-grained topology, it might
> immediately crash the simulations similar to the problem you
> described. The csg_map will give a reasonable initial structure, this
> should do well if your coarse-grained potentials are ok (eventually do
> a steep before). The topology generation (csg_gmxtopol) just provides
> a point to start from but will always require tuning by hand to put in
> correct parameters.
>
> Also verify your mapping by loading atomistic + coarse-grained
> structures in vmd.
>
> 2011/7/1 chemistry <[email protected]>:
>
> > Sorry, it was a problem with the internet and that's why I posted the
> > same message twice.
>
> > I'm doing it in the same way how you wrote. So, I'll check all stuff
> > again and thanks for fast answer.
>
> > Kind regards.
>
> > On Jul 1, 11:14 am, chemistry <[email protected]> wrote:
> >> Hello!
>
> >> Seems that I have not a good initial CG-structure. I've got it with
> >> the help of csg_map:
>
> >> $csg_map --top topol.tpr --trj traj.trr --cg mappin.xml --out cg.gro
>
> >> In my mappin.xml file every monomer of my system (P3HT) divided on the
> >> three beads and each bead has a different name.
> >> How exactly did you get initial CG-structure for propene in your
> >> example?
>
> >> Thanks a lot in advance,
> >> Sergio
>
> >> On Jun 30, 12:20 pm, Sebastian <[email protected]> wrote:
>
> >> > Hi 'chemistry',
>
> >> > it seems your bond is streching to far, this could be due to a too
> >> > weak minimum in the bonded interaction or beacause your system
> >> > explodes (too high energies) in some other part of the system.
> >> > I would try:
> >> > 1) run a steepest decent before the actual simulation
> >> > 2) make the bonded table longer by filling up some zeroes. Then check
> >> > if something else breaks (with a 'out of range') error....
>
> >> > -Sebastian
>
> >> > On Jun 30, 10:34 am, chemistry <[email protected]> wrote:
>
> >> > > Hello!
>
> >> > > Thanks again for advices. It's helped me a lot.
> >> > > I have already created all files what I need for CG calculation. But
> >> > > now I have a problem with a tabulated bond interaction. I've checked
> >> > > already this problem on the gromacs mailing-list. Unfortunately they
> >> > > do not have any good advice there how to solve this problem. I would
> >> > > be very grateful if you can give me some advice how to solve it. I
> >> > > have next error message:
>
> >> > > "Fatal error:
> >> > > A tabulated bond interaction table number 2 is out of the table range:
> >> > > r 0.646802, between table indices 646 and 647, table length 501"
>
> >> > > Thanks a lot in advance,
> >> > > Sergio.
>
> >> > > On Jun 27, 6:33 pm, Victor Ruehle <[email protected]> wrote:
>
> >> > > > 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
>
> ...
>
> read more »
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