Please have a look over this plot which is a comparision of distribution function of angles by AA and CG model.
On Friday, September 9, 2016 at 5:09:01 PM UTC+5:30, ArS wrote: > > 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? If there is any other way to modify the coarse-grained > distribution, please suggest me. How can I shift the angle distributions? > -- 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.
