2016-09-09 5:39 GMT-06:00 ArS <[email protected]>: > 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]. > 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. > -- 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.
