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 <[email protected]> wrote: > Hey, > > can you please attach your table_?.xvg > > Cheers, > Victor > > 2011/7/4 chemistry <[email protected]>: > > > 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 > > ... > > 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.
