Improper Dihedrals

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1

Dear all

My question here is two fold: one is related to improper style and other is related to vmd topotools generating impropers (dont know whether i should post here or in vmd posts. since questions are related i am posting here).

  1. In LAMMPS manual it is written “Alternatively, you can think of atoms J,K,L as being in a plane, and atom I above the plane, and X as a measure of how far out-of-plane I is with respect to the other 3 atoms.” With reference to the figure which is a simple styrene molecule, (atom ids are given in the figure). I am understanding it as say I want to write improper around atom id 7 (sp3 carbon above the benzene molecule) I would write my improper file as

1 1 7 17 18 1

This would imply that these four atoms form an improper with planes of 17-7-1 and 17-1-8 at some improper angle phi. Is this correct? Or the ordering of the atom ids do not matter?

  1. After I generate the pdb file and load into vmd. When I do

topo guessimpropers

it is generating an improper between atomids 7-1-6-2. It is written specifically that impropers are calculated when an atom is exactly bonded by 3 other atoms when in a plane. However, if the naming convention is correct, then 7-1, 7-6 and 7-2 are not connected (1-7, 1-2 and 1-6 are however). So again does the order matter? Moreover the type in improper coefficients correspond to reading the improper in reverse order (compare line 52 and 161).

As a follow up question, I want to have impropers to mimic a force field between atom ids 7-17-8-1, i.e, the sp3 carbon above benzene should hold a tetrahedral shape. Is it possible to do in VMD since guessimpropers seems not to find that set?

Thanks alot in advance. Sorry if it is a lot in one single email.

Thanks

Vaidyanathan M S

isocheck.lammps (2.74 KB)

psstructure.jpg

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Hi Arun,

Thanks alot for the help. However regarding the second point, what you said lead to my problem as well.

If i understand correctly, if the improper ids are ordered as

improperid impropertyp atom1 atom2 atom3 atom4, this means that atom1 is connected to atom2, atom3 and atom4. Or in other words, atom1 is the “central” atom and has bond connectivity between all other atoms. I am asking this again because I am still confused as to where the position of atom1 in the improper ordering matters.

If the above statement is true, with reference to the data file and figure In the bond topology information, 1 is connected to atomids 2 6 and 7 and hence I would expect the ordering of the dihedral to be

1 1 1 2 6 7 and not 1 1 7 1 6 2. (Please see the change in atomids 7 and 1. 7 is “not bonded” to 6 directly. VMD topotools guessimpropers produces the latter.)

Hence my question is how is vmd topotools trying to put an improper between 7-1-6-2 atoms. And also the second part again as to why is it is not giving 1-2-6-7. I am really sorry if the total amount of variables are frustrating . I dont know how else to explain this.

Thanks

Vaidyanathan M S