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 at > http://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.
