2016-09-12 4:00 GMT-06:00 ArS <srivastav...@iitj.ac.in>: > 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. > Well, if simple Boltzmann inversion doesn't work you might need to do iterative Boltzmann inversion. Another reason, why the distributions are off could be that you are mixing Boltzmann-inverted potentials with the MARTINI force-field. Mixing structure-based and free-energy-based potential gives unpredictable results. To check you could study a single molecule in vacuum and compare your bonded interactions.
Christoph > > 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 <srivas...@iitj.ac.in>: >> >>> 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 votca+un...@googlegroups.com. >>> To post to this group, send email to vo...@googlegroups.com. >>> 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
