I utilized topotools package to generate the topology from a coordinate set representing some polymer chains (PMMA) to equilibrate in the molten/amorphous phase. In these molecules there are sp2 Carbons (carbonyls within ester groups) that require an improper torsion angle in order to stay planar.
I use this piece of code to generate the topology:
(((writelammpsdata uses 'resid' to generate mol index)))
for {set i 0} {$i < 100} {incr i} {
set list [atomselect top "residue $i"]
$list set resid $i
}
The bonds list is perfectly spotted by the code (angles and dihedrals as well) but when I run the the simulation with lammps the sp2 Carbons are not planar. Instead, they seem to adopt an sp3-like pyramidal geometry (like ammonia).
I have noticed that in the list of improper dihedrals generated by Topotools for the LAMMPS data file (INDEX TYPE I J K L, where I J K and L are the atoms involved in the dihedral) the C-sp2 atom at the centre is in the second position of the list (i.e., J).
However, from the LAMMPS manual page (http://lammps.sandia.gov/doc/improper_harmonic.html ) it seems that those atoms should be in the first position (i.e., I). I say this because of the sentence: "Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined between the 4 atoms".
Indeed, I solved this problem by positioning the sp2 Carbon in the first entry in the impropers list. These atoms stay reasonably planar, as they are expected to do.
Weird. This is how I would have expected it too based on my experience with CHARMM. All you'd need to do is switch the order around on line 198 and 199 of topoimpropers.tcl
I utilized topotools package to generate the topology from a coordinate set representing some polymer chains (PMMA) to equilibrate in the molten/amorphous phase. In these molecules there are sp2 Carbons (carbonyls within ester groups) that require an improper torsion angle in order to stay planar.
I use this piece of code to generate the topology:
(((writelammpsdata uses 'resid' to generate mol index))) for {set i 0} {$i < 100} {incr i} { set list [atomselect top "residue $i"] $list set resid $i }
topo retypebonds topo guessangles topo guessdihedrals topo guessimpropers tolerance 30 topo writelammpsdata myfile.lammps
The bonds list is perfectly spotted by the code (angles and dihedrals as well) but when I run the the simulation with lammps the sp2 Carbons are not planar. Instead, they seem to adopt an sp3-like pyramidal geometry (like ammonia).
I have noticed that in the list of improper dihedrals generated by Topotools for the LAMMPS data file (INDEX TYPE I J K L, where I J K and L are the atoms involved in the dihedral) the C-sp2 atom at the centre is in the second position of the list (i.e., J). However, from the LAMMPS manual page (http://lammps.sandia.gov/doc/improper_harmonic.html ) it seems that those atoms should be in the first position (i.e., I). I say this because of the sentence: "Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined between the 4 atoms".
Indeed, I solved this problem by positioning the sp2 Carbon in the first entry in the impropers list. These atoms stay reasonably planar, as they are expected to do.