how to build a staggered structure with alternating orientations.

[richhongr]

Hello! Thank you for creating such a wonderful toolkit. I have already created the .ff file, and now I want to create .gro files for both a monomer and a staggered structure with alternating orientations. Could you please guide me on how to do this? Here are the commands I used to create the .gro file so far:

1. polyply gen_params -lib gromos53A6 -o P3HT.itp -name P3HT -seq Hter:1 P3HT:10 Hter:1
2. polyply gen_coords -p P3HT.top -o melt.gro -name melt -dens 10 -back_fudge 1 -mf 0.5

[fgrunewald]

@richhongr I'm not sure what you mean by alternating orientations; you mean head to tail vs tail to tail of the P3HT?
@ricalessandri perhaps it the better person to help with this

[fgrunewald]

good question; we have been working on something like this for RNA/DNA but it's not fully implemented yet. Instead you could add an extra dihedral angle that biases this conformation. If you are not building a dense melt it should work. Perhaps as a perquisite use the following build file to make 'straighter' chains that give a better approximation to the persistence length:

[ bending ]
P3HT P3HT P3HT 8

Use the above as : polyply -b build_file.bld ... The higher you put the number the straighter the chain becomes.

Before generating the structure you need to to modify the existing .ff files by adding the following dihedral angle:

[link]
resname "P3HT"
[ atoms ]
ST1 { }
CT2 { }
+CT5 { }
+ST1 { }
[ dihedrals ]
  ST1   CT2  +CT5  +ST1   1        0.0       1.80          1  {"group": "eq dihedral", "version":"5", "ifdef": "eq_polyply"} 
[ edges ]
ST1 CT2
CT2 +CT5
+CT5 +ST1

Then generate the itp file again, the structure and run the energy minimization but put 'defines = -Deq_polyply' on the top if the MDP file. Potentially you need to run some short MD with 'defines = -Deq_polyply' to fully get what you want.

[richhongr]

Thank you for your response! However, when I use this command:
polyply gen_coords -p P3HT.top -o melt.gro -name melt -dens 10 -back_fudge 1 -mf 0.5 -b build_file.bld
It throws an error:
OSError: Can't parse line 2 in section '['bending']' because the section is unknown
How should I resolve this issue?

[fgrunewald]

@richhongr the bending is a relatively new feature. you probably have to reinstall polyply

[richhongr]

Okay, thank you for your assistance.

[fgrunewald]

@richhongr let me know if the strategy works out; it might be useful for others too