Hey,
1) I recommend to use version 1.2. The functionality + arguments of
convert_potentials have slightly changed.
2) in the files you sent me, the bad sampled regions were not cut and
therefore the extrapolate failed (zoom in at table_a0.xvg where the
extrapolated region at the left starts). This will lead to a very
strong peak in the force and is probably what messes up your run.
Please make sure to really cut the very rough points at the left and
right of bonded potentials. This was done in the sed commands i send
you. Either adjust the number of points there or better skip this
command and do it manually.
Victor
2011/7/5 chemistry <donets1...@gmail.com>:
> Hey,
>
> the format of the table_*.xvg which was created after post-processing
> looks like this:
>
> table_a1.xvg:
>
> 0.0000000000e+00 8.6955642509e+07 0.0000000000e+00
> 5.0000000000e-02 8.6862417509e+07 1.8640000000e+06
> 1.0000000000e-01 8.6769242509e+07 1.8630000000e+06
> 1.5000000000e-01 8.6676117509e+07 1.8620000000e+06
> 2.0000000000e-01 8.6583042509e+07 1.8610000000e+06
>
> and yesterday I've created the same format of the table like in your
> case by myself. I used for this C-programing and described the
> potential with the help of harmonic potential. And now it works well.
>
> new one table_a1.xvg:
>
> 0.000000 1201.461834 0
> 0.050000 1200.343519 0
> 0.100000 1199.225724 0
> 0.150000 1198.108451 0
> 0.200000 1196.991698 0
>
> In both cases the potentials look similar around the minimum. Is it
> possible that the GROMACS in someway cannot read correctly the
> table_*.xvg?
>
> Kind regards,
> Sergio
>
>
> On Jul 4, 7:50 pm, Victor Ruehle <rue...@votca.org> wrote:
>> Hey,
>>
>> can you please attach your table_?.xvg
>>
>> Cheers,
>> Victor
>>
>> 2011/7/4 chemistry <donets1...@gmail.com>:
>>
>> > 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 <rue...@votca.org> 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 <donets1...@gmail.com>:
>>
>> >> > 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 <donets1...@gmail.com> 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 <frit...@mpip-mainz.mpg.de> 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 <donets1...@gmail.com> 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 <rue...@votca.org> 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 <donets1...@gmail.com>:
>>
>> >> >> > > > > 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 <jungh...@votca.org>
>> >> >> > > > > 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 <donets1...@gmail.com>:
>>
>> >> >> > > > >> > 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 <jungh...@votca.org>
>> >> >> > > > >> > 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
>>
>> ...
>>
>> read more »
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To post to this group, send email to votca@googlegroups.com.
> To unsubscribe from this group, send email to
> votca+unsubscr...@googlegroups.com.
> 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 votca@googlegroups.com.
To unsubscribe from this group, send email to
votca+unsubscr...@googlegroups.com.
For more options, visit this group at
http://groups.google.com/group/votca?hl=en.
