PS melt simulation

[Rituparnasamanta]

Hi team
I am doing coarse-grained simulations of polystyrene melts with the itp files generated from polyply. Although our results match for the end to end distances, as mentioned in Rossi et al. in their Martini 2 polystyrene paper. However, the melt density is around double of what they see (which is 951kg/m3). From what I understand, the bonded parameters are unchanged, and the bead type becomes that in Martini3. I also checked the reference (#379) provided in a previous discussion regarding this issue, and saw that your the reported density from Martini3 for PS is also around 2000kg/m3. Could you please comment or share your thoughts on why it might be so different?

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Rituparna

[ricalessandri]

Hi Rituparna - two potential issues that should be checked:

1. make sure you're using the latest PS model (https://github.com/marrink-lab/polyply_1.0/blob/master/polyply/data/martini3/vinyl_polymers.ff#L240-L274). If you have installed the latest polyply version, you'd get the latest PS model by doing:

  polyply gen_params -library martini3 -seq STYR:100 -o PS_n100.itp -name PS

2. make sure to use the actual mass of the PS repeat unit when computing the density and not the default Martini masses because that would lead to an overestimation of the density. You need to create a PS_n100_MM.itp where the mass of the repeat unit is distributed on the beads.
   Hope this helps

[Rituparnasamanta]

PS_n100_styrff.txt
Thank you. I have changed both and obtained a density that is not far from the experimental melt density. I have uploaded the new itp file for your reference. I would like to know your comments. I have a few questions.

1. My first question is about point 2, adding the actual mass of the repeat units. For the ITP files generated by Polyply, we either have a vacant column for mass or a default value of the martini masses. What is the value of mass taken when there is a vacant column for mass? Are you suggesting we should always populate that column based on the corresponding repeat unit?
2. My second question is about the PS itp file, the bond coefficient for vnl-vnl, and also the bond angles are different from the previous PS itp file. The previous ones were closer to the Rossi et al. Is there any reasoning behind the new vinyl_polymers.ff?

[ricalessandri]

Great. To you questions:

1. If no masses are given in the PS.itp, then Gromacs takes the (default) bead masses are taken from the martini_v3.0.0.itp.
2. These have been re-parametrized by @fgrunewald (preprint coming). The reason is that the (sizes of the) beads are different in this model than in the Martini 2 model of Rossi. For full details, while waiting for a preprint, perhaps @fgrunewald can comment or you could take a look at chapter 5 of his phd thesis (https://pure.rug.nl/ws/files/756637593/Complete_thesis.pdf).