Hello, Victor! Is it possible do not use tables_*.xvg and instead of it set the parameters for bond, angle and dihedral to the topol.top with equilibrium bond length, angle and force constants. In this case ibi- procedure for my system works. And how one can choose the exact simulation time for one iteration for different systems?
Thanks a lot in advance, Sergio On Jul 5, 5:04 pm, Victor Ruehle <[email protected]> wrote: > Hey, > > 1) I recommend to use version 1.2. The functionality + arguments of > convert_potentials have slightly changed. > > 2) in the files you sent me, the bad sampled regions were not cut and > therefore the extrapolate failed (zoom in at table_a0.xvg where the > extrapolated region at the left starts). This will lead to a very > strong peak in the force and is probably what messes up your run. > Please make sure to really cut the very rough points at the left and > right of bonded potentials. This was done in the sed commands i send > you. Either adjust the number of points there or better skip this > command and do it manually. > > Victor > > 2011/7/5 chemistry <[email protected]>: > > > 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> > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "votca" group. 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