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lenhanpham / MoSu-CHARMM

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how to generate the top file for MoS2 of arbitrary size #1

Open MrZLY opened 1 week ago

MrZLY commented 1 week ago

Hello author,

I am a beginner, and I would like to use your force field to simulate 2D MoS2. However, I am unsure how to generate the corresponding top file for a PDB file of MoS2 of arbitrary size（I need 10x10nm）. On one hand, as you mentioned, pdb2gmx requires residue names, making it impossible to generate the top file directly. On the other hand, x2top requires n2t files . I also encountered the error "Could only find a forcefield type." Moreover, in the PDB file I created, there are only three atom types, Mo, S1, and S2, which makes it difficult to manually change them to the six types used in the force field.

Is there a simpler way to generate the top file corresponding to the PDB file of a monolayer MoS2 using your force field? Thank you.

lenhanpham commented 4 days ago

Hi there,

Doing MD simulations is a bit complicated, especially for beginners. It is better that you can understand all things related to do an MD simulation. What I can say now is that in MoSu-CHARMM, there are basically two atom types (Mo and S), but depending on one's purposes, duplicated of these atom types can be created to include bonded functions in the force field. All non-bonded and bonded parameters of MoS2 adopted from other papers can be seen in the itp files of MoS2.

MoS2 itp files should be generated depending on size and termination atoms of the sheet. So, you have to do it yourself. Winmostar migh be helpful here, but you have to do a lot to get ipt generated by winmostar adapted to the parameter sets of well developed force fields (for example the ones I used in this paper https://pubs.rsc.org/en/content/articlehtml/2024/tb/d4tb01127a) https://winmostar.com/en/

Good luck with your work.

MrZLY commented 2 days ago

Hi author,

Thank you very much for your help and valuable advice! I will follow your suggestions and work on generating the corresponding itp files. I also appreciate the article and tool recommendations you shared, and I will review them carefully. Wishing you continued success in your research.