Dear VOTCA users, I am coarse graining a surfactant molecule. I am deriving the bonded potentials using IBI. 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.
Thjs 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 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. -- 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.
