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. > > > >> > On Jun 7, 1:22 pm, Christoph Junghans <[email protected]> wrote: > > >> >> 2011/6/7 chemistry <[email protected]>:> Under "nothing happens" I > > >> >> meant that after execution the command > > >> >> > $ csg_inverse settings.xml (I'm using version 1.1.1) > > >> >> > I have message: "end". And I do not have any created dir (step_000) > > >> >> > or > > >> >> > files (like inverse.log...). > > > >> >> Very strange! Please run > > >> >> $ bash -x `which csg_inverse` settings.xml > > >> >> and post the output. > > > >> >> Cheers, > > > >> >> Christoph > > > >> >> > But when I'm using > > > >> >> > $ csg_stat --top topol.tpr --trj traj.xtc --options settings.xml > > >> >> > --cg > > >> >> > propane.xml > > > >> >> > for computing RDF's for propane it works with the same > > >> >> > "settings.xml" > > >> >> > file and I have created A-A.dist.new for A-A... > > >> >> > Is it possible that I have some problem with a link to the gromacs > > >> >> > and > > >> >> > VOTCA cannot start iterative procedure? > > > >> >> > Thanks a lot in advance. > > >> >> > Sergio > > > >> >> > On Jun 6, 10:56 am, Christoph Junghans <[email protected]> wrote: > > >> >> >> Hi Sergio, > > > >> >> >> can you be a bit more explicit, what (not) happens? > > >> >> >> I quickly tested the propane tutorial: > > >> >> >> $ pwd > > >> >> >> $HOME/votca/src/tutorials/propane/ibi > > >> >> >> $ csg_inverse --options settings.xml #for version 1.1 remove > > >> >> >> --options > > >> >> >> For a more verbose log see: inverse.log > > >> >> >> We are doing Method: ibi > > >> >> >> Prepare (dir step_000) > > >> >> >> Using initial guess from dist A-A.dist.tgt for A-A > > >> >> >> ... > > > >> >> >> It seems to work for me. > > >> >> >> Which version are you using? (see csg_stat --help) > > >> >> >> Which command did you execute to start ibi? > > > >> >> >> Cheers, > > > >> >> >> Christoph > > > >> >> >> 2011/6/6 chemistry <[email protected]>: > > > >> >> >> > Hello all!!! > > > >> >> >> > I'm just started to use votca and at the moment I'm going threw > > >> >> >> > the > > >> >> >> > tutorial. But I've got some problem with IBI procedure. In > > >> >> >> > general I > > >> >> >> > understood what mean every parameter in the "setting.xml" file > > >> >> >> > but I > > >> >> >> > have a problem when I'm trying to submit the calculation: nothing > > >> >> >> > happened. Can anyone tell me what exactly I may have missed in > > >> >> >> > the > > >> >> >> > standart "setting.xml" file for propane. I'll appreciate any > > >> >> >> > advise, > > >> >> >> > thanks a lot in advance! > > > >> >> >> > Sergio > > > >> >> >> > -- > > >> >> >> > 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 > > >> >> >> > athttp://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]. > > >> >> > For more options, visit this group > > >> >> > athttp://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]. > > >> > For more options, visit this group > > >> > athttp://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]. > > > For more options, visit this group > > > athttp://groups.google.com/group/votca?hl=en. > > -- 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.
