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 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 >> >> ... >> >> 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. > > -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. 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