Cavity Energetic Sizing Algorithm (CESA) analysis for polymers - from Material Studio to EMC

EMC
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Hi everyone,

I am reaching out because I am very interested in utilizing the CESA algorithm within EMC to analyze the void size distribution of polymers in a membrane matrix.

Currently, my workflow involves equilibrating my polymer systems in Materials Studio. I am hoping to bring those files over to EMC to perform CESA analysis directly. I have downloaded the EMC package from SourceForge and I am running it via Ubuntu on WSL2. But being very new to EMC, I am not entirely sure of the best way to do this.

Could anyone please point me in the right direction regarding the file compatibility or the import process? Furthermore, after importing to EMC, how could I conduct the CESA run? Any help would be immensely appreciated.

Thanks in advance your your patience!

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Hi @JesseJiaCheng you can use GitHub - askforarun/PoreBlazer_OpenMP: PoreBlazer optimized source code, examples, and geometric properties of porous materials · GitHub (check it out) for FFV and FFV distribution

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Albeit there are other codes to quantify void space, the question at hand pertains to CESA specifically. CESA is available as part of ITEM ANALYZE. You can build and run your systems with EMC in a normal fashion (see e.g. emc_template.sh polymer polymer and emc_template environment setup and the resulting polymer.esh and setup.esh as starting points, incorporating polymer.esh into the ITEM TEMPLATE section of setup.esh). You would have to add

# Analysis section

ITEM	ANALYSIS

cavity		active=true

ITEM	END	# ANALYSIS

to setup.esh. You can find the EMC Script used for analysis at $EMC_ROOT/scripts/analyze/cavity.esh. This script assumes the existence of an EMC structure file and a trajectory in standard LAMMPS dump format.

Conversely, if you are inclined to use already existing .car and .mdf InsightII files as exported by Materials Studio, you can translate these into a trajectory file and an EMC structure file with EMC. This procedure depends on having a valid force field, since CESA uses energetics to determine void size. I would need to know more details about your Materials Studio simulation to say anything more substantial.

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Thank you very much for your suggestion! I’ll look into it!

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Hi Dr Veld,

Thank you for your kind reply!

To provide you with more details regarding my Materials Studio simulation: I am using the COMPASS force field, and my system is an amorphous Mixed Matrix Membrane (MMM) cell consisting of a polymer matrix (polysulfone) embedded with a filler (silica).

I have a single equilibrated frame following a MD run through COMPASS force field, which is saved as Equilibrium.car and Equilibrium.mdf.

Since I am new to the EMC environment, could you please provide a sample script or a template showing how to import these specific .car and .mdf files, map them to the COMPASS force field to translate them into native EMC structure/trajectory files, and subsequently pass them into the CESA analysis code?

Thank you so much for your time and help!

Best regards,
Jesse