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. 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.
