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 >> >> >> > 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. > > -- 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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