Thanks a lot, it helps!!! On Mar 19, 5:22 pm, Christoph Junghans <[email protected]> wrote: > Am 19. März 2012 10:12 schrieb chemistry <[email protected]>: > > > Do You mean in the topol_cg.top? > > .......... > > [ moleculetype ] > > ; Name nrexcl > > P3HT 3 > > ......... > > > to change 3 to 4 (to exclude 1-5 interaction) and call grompp as: > > > $ grompp -f -c -n -p topol_cg.top -o topol_excl.tpr > > > In this case i have two *.tpr files: topol.tpr for CG MD simulation > > and topol_excl.tpr for "csg_stat". Now i have a question: where > > exactly i should define that "csg_stat" must take topol_excl.tpr to > > calculate RDF's and "mdrun" must take topol.tpr for the cg- > > simulation. > > Well, if you want to execute csg_stat a single time, you may specify > it by hand (--top option). > > For csg_inverse there is an extra option to specify a different tpr > file to calculate the rdfs. > Specify the name in "cg.inverse.gromacs.rdf.topol" in seetings.xml and > remember to add the file to "cg.inverse.filelist" so that it get > copied in every step. > > Christoph > > > > > > > On Mar 19, 1:19 am, Christoph Junghans <[email protected]> wrote: > >> Hi Sergii > > >> Am 18. März 2012 14:22 schrieb chemistry <[email protected]>:> Hello > >> dear developers of votca!!! > > >> > I'm using votca-1.2.2 for "ibi" and i have question related to the > >> > multi_g_rdf. Is it possible to exclude intramolecular (like 1-5 and > >> > futher...) interactions from the RDF's and to count just > >> > intermolecular interactions? Because i have additional hill on my rdf > >> > which correspond to the 1-5 intramolecular interaction. Does it have a > >> > big influence on the final set of the potentials? > > >> You have to generate a second tpr file with the required exclusions. > >> Then call multi_g_rdf as: > >> $ multi_g_rdf -e XX -8 -- -s topol_excl.tpr > > >> As a side remark, I would recommend using csg_stat instead of > >> multi_g_rdf as it is much faster for bigger systems (grid search (N) > >> instead of N**2 search). > >> And it saves you mapping the trajectory to cg first as csg_stat has > >> the functionality of csg_map build-in. > >> $ csg_stat --cg map.xml --nt 8 --trj atomistic.xtc --top atomistic.tpr > >> --options seetings.xml > >> or use it on the cg trajectory > >> $ csg_stat --nt 8 --trj cg.xtc --top cg.tpr --options seetings.xml > > >> Cheers, > > >> Christoph > > >> > Thanks a lot in advance for your response, > > >> > sincerely > >> > Sergii > > >> > -- > >> > 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. > > >> -- > >> Christoph Junghans > >> Web:http://www.compphys.de > > > -- > > 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. > > -- > Christoph Junghans > Web:http://www.compphys.de
-- 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.
