Hello! in U(n+1) = U(n) + ai*kb*T*ln(P(n)/P(ref)) where one can set numerical factor ai (0<ai<1). At the moment my calculation is diverges, so in general how one can reach better convergency?
Kind regards, Sergio On Jul 7, 5:03 pm, Christoph Junghans <[email protected]> wrote: > 2011/7/7 chemistry <[email protected]>:> 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. > > Yes, if the potential can be reasonably approximated by a harmonic > form. Just compare the table to k/2*(r-r_0)^2 ! > > > And how one can choose the exact simulation time for one iteration for > > different systems? > > There is no rule. The iteration has to be long enough, so that the > distributions of the interactions, you want to iteratively refine, are > sampled reasonable. Too long iterations just waste your computer time > ;-) > I usually do 100 short iterations follow by 50 longer ones, but that > is my personal recipe. > > Cheers, > > Christoph > > > > > 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 > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "votca" group. 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