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 > >> >> > iterations: > > >> >> > csg_stat --top topol.tpr --trj traj.xtc --options settings.xml --cg > >> >> > mapping.xml > > >> >> > I have P3HT system. Every monomer divided on the three beads. > >> >> > Thiophene ring represented the first bead and hexyl chain divided on > >> >> > the two beads - each bead include three carbon atoms. > > >> >> > in the settings.xml file I specified the types of the beads which are > >> >> > the same like in the mapping.xml: > > >> >> > ............. > >> >> > <non-bonded> > >> >> > <!-- name of the interaction --> > >> >> > <name>P1-P1</name> > >> >> > <!-- types involved in this interaction --> > >> >> > <type1>A</type1> > >> >> > <type2>A</type2> > >> >> > <!-- dimension + grid spacing of tables for calculations --> > >> >> > <min>0</min> > >> >> > <max>1.36</max> > >> >> > <step>0.01</step> > >> >> > <inverse> > >> >> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > >> >> > <target>P1-P1.dist.tgt</target> > >> >> > <!-- update cycles --> > >> >> > <do_potential>1 0 0</do_potential> > >> >> > <!-- additional post processing of dU before added to potential > >> >> > --> > >> >> > <post_update></post_update> > >> >> > <!-- additional post processing of U after dU added to potential > >> >> > --> > >> >> > <post_add></post_add> > >> >> > <!-- name of the table for gromacs run --> > >> >> > <gromacs> > >> >> > <table>table_P1_P1.xvg</table> > >> >> > </gromacs> > >> >> > </inverse> > >> >> > </non-bonded> > >> >> > ............... > > >> >> > ---mapping.xml---: > > >> >> > <cg_molecule> > >> >> > <name>P3HT</name> > >> >> > <ident>Protein_X</ident> > >> >> > <topology> > >> >> > <cg_beads> > >> >> > <cg_bead> > >> >> > <name>S1</name> > >> >> > <type>A</type> > >> >> > <symmetry>1</symmetry> > >> >> > <mapping>A</mapping> > >> >> > <beads> 1:BBB:S01 1:BBB:C01 1:BBB:C02 1:BBB:H01 1:BBB:C03 > >> >> > 1:BBB:C04 1:BBB:H02 </beads> > >> >> > </cg_bead> > >> >> > ................ > > >> >> > Also I specified all <bonds> and <angles> and <weights>. It works > >> >> > well, but the second nearest neighbor does not excluded from the rdf. > >> >> > Seems that the exclusion works just for the first nearest neighbor. Is > >> >> > it possible to exclude this interaction from the rdf? > > >> >> > On Jun 17, 11:11 am, Victor Rühle <[email protected]> wrote: > >> >> >> Hey, > > >> >> >> Can you please describe you problem in more details, what exactly did > >> >> >> you try? Are you referring to calculating the target rdf, or the rdf > >> >> >> in > >> >> >> the iterations? > > >> >> >> We introduced proper exclusion handling in version 1.1, so it should > >> >> >> work. You can check whether exclusions are read correctly by: > > >> >> >> csg_dump --top topol.tpr --excl > > >> >> >> or if you use csg_stat to calculate target rdf: > > >> >> >> csg_dump --top topol.tpr --cg mappin.xml --excl > > >> >> >> If you use g_rdf, you have to specify the topology -s topol.tpr in > >> >> >> addition to an index file. > > >> >> >> A brief side-note: > >> >> >> Be aware, that for the reference rdf and that during the iterations, > >> >> >> the > >> >> >> exact identical normalization should be used (there is room for some > >> >> >> discrepancy, however as far as i could see it's more problematic for > >> >> >> IMC > >> >> >> than for IBI). Therefore better use the same program for both > >> >> >> (csg_stat > >> >> >> to calculate reference). In version 1.2, which was released > >> >> >> yesterday, > >> >> >> we have adjusted the normalization to be identical to g_rdf in > >> >> >> gromacs 4.5. > > >> >> >> Victor > > >> >> >> On 06/17/2011 10:32 AM, chemistry wrote: > > >> >> >> > I have one addition question about the ibi procedure. I have a > >> >> >> > polymer > >> >> >> > chain and I'm doing ibi for non-bonded interactions. How can I > >> >> >> > exclude > >> >> >> > the bond part from the RDF? Because in my case I have all the same > >> >> >> > beads in the backbone chain of my polymer and when I'm calculating > >> >> >> > the > >> >> >> > RDF it does not correspond to the purely non-bond interactions. > >> >> >> > This > >> >> >> > RDF except the non-bonded part includes the bonded part. > > >> >> >> > Thanks a lot in advance. > >> >> >> > Sergio > > >> >> >> > On Jun 14, 2:59 pm, chemistry <[email protected]> wrote: > >> >> >> >> Thanks a lot for advice. Now ibi procedure works. > > >> >> >> >> On Jun 9, 8:31 pm, Victor Ruehle <[email protected]> wrote: > > >> >> >> >>> Hey, > >> >> >> >>> did you source your VOTCA installation? > >> >> >> >>> source /votca-tools-1.1.1/bin/VOTCARC.bash > >> >> >> >>> And if you manually installed gromacs that as well? If you still > >> >> >> >>> don"t > >> >> >> >>> get it running > >> >> >> >>> bash -x /votca-tools-1.1.1/bin/csg_inverse settings.xml > >> >> >> >>> and send the output. > >> >> >> >>> Cheers, > >> >> >> >>> Victor > >> >> >> >>> 2011/6/9 chemistry <[email protected]>: > >> >> >> >>>> Seems that yes. In the folder "/votca-tools-1.1.1/bin/" I have > >> >> >> >>>> installed "csg_inverse" and all another tools. > >> >> >> >>>> For installation of VOTCA I used "./build.sh". I installed > >> >> >> >>>> additionally GROMACS with shared lib (*.so), because at the > >> >> >> >>>> beginning > >> >> >> >>>> it was a problem. > >> >> >> >>>> On Jun 8, 1:38 pm, Christoph Junghans <[email protected]> > >> >> >> >>>> wrote: > >> >> >> >>>>> 2011/6/8 chemistry <[email protected]>:> After run > >> >> >> >>>>>> $ bash -x `which csg_inverse` settings.xml > >> >> >> >>>>>> I've got this message: > >> >> >> >>>>>> "bash: csg_inverse:: No such file or directory" > >> >> >> >>>>> It seems like your installation is broken. How did you install > >> >> >> >>>>> your > >> >> >> >>>>> VOTCA version? > >> >> >> >>>>> Is there a csg_inverse installed? > >> >> >> >>>>> Cheers, > >> >> >> >>>>> Christoph > >> >> >> >>>>>> I tried to set the path to the "csg_inverse" and gromacs > >> >> >> >>>>>> directly in > >> >> >> >>>>>> the "settings.xml" but it does not help. > > ... > > 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.
