I meant that is there any method to modify the tabulated angle potentials, which are generated by inversion Boltzmann distribution? I think that my angle potentials are wrong and hence the angular distribution due to the AA simulation and those obtained after the coarse-grained simulation are mismatched.
On Friday, September 9, 2016 at 8:26:07 PM UTC+5:30, Christoph Junghans wrote: > > > > 2016-09-09 5:39 GMT-06:00 ArS <[email protected] <javascript:>>: > >> Dear VOTCA users, >> >> I am coarse graining a surfactant molecule. I am deriving the bonded >> potentials using Boltzmann inversion. First I got the distributions of >> bonds and angles due to mapping of atomistic model to a coarse-grained >> model, and from those distributions, bonded potentials were derived. >> Then those potentials were used during the simulation. The non-bonded >> potentials are obtained using the MARTINI force-field. After the 20 ns NPT >> run of the coarse-grained system, I again checked for the distributions of >> bonds and angles. While comparing the distributions due to AA-model and the >> CG-model, the bond distributions match well but the angle distributions do >> not. Specially for the head bead, the angle distribution is very different. >> >> This is how I generated the angle distributions by mapping AA model to CG >> model: >> >> cat boltzmann_btm_analysis_angle_shape | csg_boltzmann --top >> ../../../npt.tpr --trj ../../../npt-180ns.xtc --cg ../btm.xml --map-ignore >> "STE;Cl;SOL" >> >> The "boltzmann_btm_analysis_angle_shape" is written as: >> >> hist angle.dist.ib *:angle1:* >> tab set T 283 >> tab set scale angle1 >> tab angle.pot *:angle1:* >> q >> >> After a run 0f 20 ns, the angle distribution of the coarse-grained model >> is generated as: >> cat boltzmann_shape | csg_boltzmann --top ../table.tpr --trj >> ../table.xtc --cg map_btm.xml --map-ignore "STE;CL-;W" >> >> The boltzmann_shape is written as: >> hist bond.without_shift_btm1.ib *bond1:* >> hist bond.without_shift_btm2.ib *bond2:* >> hist bond.without_shift_btm3.ib *bond3:* >> hist bond.without_shift_btm4.ib *bond4:* >> hist bond.without_shift_btm5.ib *bond5:* >> hist angle.without_shift_btm1.ib *angle1:* >> hist angle.without_shift_btm2.ib *angle2:* >> >> hist angle.without_shift_btm3.ib *angle3:* >> hist angle.without_shift_btm4.ib *angle4:* >> q >> >> While generating the tables for bonded and anglular potentials, I used >> csg_resample command, in the --grid option, I used step of 0.002 (example >> : --grid 0.00:0.002:3.142). Similarly, while exporting the tables using >> csg_call --options, in the table.xml file, table_bins value is 0.002. >> If I change the step and the table_bins values, can I get a better angle >> potential so that the angle distribution of CG model matches with that of >> the AA model? >> > I am afraid no, changing the bins sizes does very little to the potential > and hence the distribution. Making the bins size smaller might help to > resolve some peaks better, but it won't help with the shoulders of the > distribution. > > >> If there is any other way to modify the coarse-grained distribution, >> please suggest me. >> > Use a different coarse-graining technique, e.g. force matching. > > >> How can I shift the angle distributions? >> > What do you mean by shifting? > > Christoph > > -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
