2016-03-31 5:53 GMT-06:00 Takahiro Ohkuma <[email protected]>: > Dear all > > Sorry for bothering you. Maybe, I found my mistake. I should use "tab set > scale no" insted of "tab set scale angle" in case of dihedrals? Yes, the scale sets the normalization factor, i.e. the volume element, see Eq. 5 of the VOTCA paper (J. Chem. Theo. Comp. 5, 3211 (2009)). And for dihedrals the normalization is 1, so "scale no" is correct. Also see the build-in help of csg_boltzmann ("help tab set scale").
Christoph > > Best > Takahiro > > 2016年3月31日木曜日 12時51分11秒 UTC+2 Takahiro Ohkuma: >> >> Dear developers and users >> >> I have a problem in calculating the dihedral potential by csg_boltzmann >> and I do not know how to solve it. My system contains linear polymers made >> of only B-type beads. >> The "dihedral-BBBB.pot" file is obtained by the blow commands, but it does >> not consistent with the distribution function that is obtained by csg_map >> command. At the point of lower probability, the potential energy gets lower >> value as shown in the attached png file. >> In addition, in a x range of [-3.1415, 0], nans appear in "the >> dihedral-BBBB.pot" file. >> >> $ csg_boltzmann --trj traj.trr --top md393K_1.tpr --cg UIP24.xml >> > tab set T 393 >> > tab set scale angle >> > tab set min -3.1415 >> > tab set max 3.1415 >> > tab dihedral-BBBB.pot *:dihedral-BBBB:* >> >> Thank you for your help. >> >> > -- > 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.
