Hello! Seems that I have a problem with my CG-structure. I've got this structure from all-atom simulation with the help of the csg_map:
$csg_map --top topol.tpr --trj traj.trr --cg mappin.xml --out cg.gro In the mappin.xml file every monomer of my system (P3HT) divided on three beads and each bead in my polymer has different name (I have 12 monomers in my polymer-chain). How exactly did you get the CG-structure for propane in your example? Thanks a lot in advance, Sergio On Jun 30, 12:20 pm, Sebastian <[email protected]> wrote: > Hi 'chemistry', > > it seems your bond is streching to far, this could be due to a too > weak minimum in the bonded interaction or beacause your system > explodes (too high energies) in some other part of the system. > I would try: > 1) run a steepest decent before the actual simulation > 2) make the bonded table longer by filling up some zeroes. Then check > if something else breaks (with a 'out of range') error.... > > -Sebastian > > On Jun 30, 10:34 am, chemistry <[email protected]> wrote: > > > Hello! > > > Thanks again for advices. It's helped me a lot. > > I have already created all files what I need for CG calculation. But > > now I have a problem with a tabulated bond interaction. I've checked > > already this problem on the gromacs mailing-list. Unfortunately they > > do not have any good advice there how to solve this problem. I would > > be very grateful if you can give me some advice how to solve it. I > > have next error message: > > > "Fatal error: > > A tabulated bond interaction table number 2 is out of the table range: > > r 0.646802, between table indices 646 and 647, table length 501" > > > Thanks a lot in advance, > > Sergio. > > > On Jun 27, 6:33 pm, Victor Ruehle <[email protected]> wrote: > > > > Hey, > > > > i also use csg_boltzmann, the tab command (dont forget tab set scale > > > bond / tab set scale angle for bond/angles). some of my examples (the > > > .pot files are the output of csg_boltzmann): > > > bonds: > > > cp ../../pot/AB_bond.pot . > > > sed -e '1,5d' -e 's/$/ 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.
