2011/7/1 chemistry <[email protected]>: > 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? I didn't get what exactly is your question. The above csg_map command looks correct to me. View the cg.gro (maybe with VMD) to see if the mapping was done correctly.
To start an ibi simulation you will need: -initial configuration (your cg.gro) - make sure that cg.inverse.gromacs.conf in your option xml file has the same value, as 'conf.gro' is the default name. -gromacs run parameter file (grompp.mdp) -gromacs text topology (topol.top) - output of csg_gmxtopol can be used a starting point -gromacs index file (index.ndx) - run make_ndx on cg initial configuration -target distributions (filenames inverse.target inside the interaction block) in the xml setting file -any additional files (bonded tables, table.xvg) to make gromacs happy - add them to inverse.filelist For details please have a look at the manual: <http://votca.googlecode.com/files/votca-manual-1.2.pdf> Cheers, Christoph > > 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. > > -- Dr. Christoph Junghans Votca Core Developer Web: http://www.votca.org -- 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]. 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