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 > > > >> >> >> > 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 > > ... > > 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.
