search

marrink-lab / polyply_1.0

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
Apache License 2.0
119 stars 21 forks source link

PEO end-groups in Martini3 #366

Closed CdG1999 closed 2 months ago

CdG1999 commented 2 months ago

Hi! Thank you very much for the polyply program, it works like a charm. However, my research focuses on studying PEO systems and their interactions in various environments. To do this, I used Martini2 as well as Martini3. In Martini2, the OH end-groups are illustrated by an SP2 bead, while in Martini3 (using polyply), no OH end-groups are used. I was wondering how Martini3 incorporates the OH-OH interactions without having the bead, as they are definitely important for the phase behavior of the system.

Regards, Christophe

fgrunewald commented 2 months ago

@CdG1999 happy to hear that you like polyply. For Martini3 you can add OH endgroups if you need them. Otherwise the molecule represents PEO with CH3 terminal groups. 

polyply gen_params -lib martini3 -seq OHter:1 PEO:#n OHter:1 -o PEO_OH.itp -name PEO

Does that solve your porblem / answer your question.

CdG1999 commented 2 months ago

@fgrunewald Exactly what I needed, thanks!