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 > >> >> >> > 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> > >> >> >> >> > > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "votca" group. 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