On Tuesday, December 2, 2014 4:47:22 PM UTC+1, Christoph Junghans wrote: > > 2014-12-01 18:11 GMT-07:00 Vitalie Botan <[email protected] > <javascript:>>: > > Most of the code is already there, it is just not enabled, because I > have never used tabulated bonded interaction in LAMMPS. > Do you have a specification for LAMMPS' bonded tables? (i.e. what's > in the 1st, 2nd, 3rd column for bond, angle and dihedral tables?) >
Hi Christoph, Thanks for the prompt reply, it seems I overlooked the fact, that gromacs version of the script produces not only xvg-table, but a normal one as well. Regarding the format of the bonded tabulated potential, it is very similar to the non-bonded format (which is already implemented in votca) with few exceptions I have copied from the Lammps manual below: 1) A section begins with a non-blank line whose 1st character is not a "#"; blank lines or lines starting with "#" can be used as comments between sections. The first line begins with a keyword which identifies the section. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. The parameter "N" is required and its value is the number of table entries that follow. Following a blank line, the next N lines list the tabulated values. On each line, the 1st value is the index from 1 to N, the 2nd value is the bond length r (in distance units), the 3rd value is the energy (in energy units), and the 4th is the force (in force units). The bond lengths must range from a LO value to a HI value, and increase from one line to the next. If the actual bond length is ever smaller than the LO value or larger than the HI value, then the bond energy and force is evaluated as if the bond were the LO or HI length. 2) For angle potential, on each line, the 1st value is the index from 1 to N, the 2nd value is the angle value (in degrees), the 3rd value is the energy (in energy units), and the 4th is -dE/d(theta) (also in energy units). The 3rd term is the energy of the 3-atom configuration for the specified angle. The last term is the derivative of the energy with respect to the angle (in degrees, not radians). Thus the units of the last term are still energy, not force. The angle values must increase from one line to the next. The angle values must also begin with 0.0 and end with 180.0, i.e. span the full range of possible angles. 3) For dihedral potential, on each line, the 1st value is the index from 1 to N, the 2nd value is the angle value, the 3rd value is the energy (in energy units), and the 4th is -dE/d(phi) also in energy units). The 3rd term is the energy of the 4-atom configuration for the specified angle. The 4th term (when present) is the negative derivative of the energy with respect to the angle (in degrees, or radians depending on whether the user selected DEGREES or RADIANS). Thus the units of the last term are still energy, not force. The dihedral angle values must increase from one line to the next. Dihedral table splines are cyclic. There is no discontinuity at 180 degrees (or at any other angle). In general, the first angle in the list can have any value (positive, zero, or negative). However the *range* of angles represented in the table must be *strictly* less than 360 degrees (2pi radians) to avoid angle overlap. (You may not supply entries in the table for both 180 and -180, for example.) If the user's table covers only a narrow range of dihedral angles, strange numerical behavior can occur in the large remaining gap. Hope these restrictions don't pose any problem for implementing in the script. Thanks in advance. Best, --Vitalie -- 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
