How to run a polymer coarse-grained simulation in VOTCA?

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Satyen Dhamankar

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May 29, 2021, 2:56:24 PM5/29/21

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Hello,

I am planning on running a coarse-grained polymer simulation of PNIPAM (40-monomer units long) using VOTCA. I have the all-atom simulation running in GROMACS, but I am trying to run the CG version using VOTCA.

I want to coarse-grain the the two carbons in the backbone into one bead, the carbonyl-amide group into another bead, and the isopropyl group into 3 distinct beads as shown in the picture below.

WhatsApp Image 2021-05-29 at 14.51.43.jpeg

My question is, if I have a 40-monomer long chain, does my .xml file need to have definitions for 40x3=120 beads? Is there a way around this?

I ask this out of curiosity. If there is no way around this, I will for sure be writing some scripts to help with the process.

Thank you for any advice you have for me! :)

Christoph Junghans

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May 29, 2021, 5:40:54 PM5/29/21

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On Sat, May 29, 2021 at 12:56 PM Satyen Dhamankar <saty...@gmail.com> wrote:

Hello,

I am planning on running a coarse-grained polymer simulation of PNIPAM (40-monomer units long) using VOTCA. I have the all-atom simulation running in GROMACS, but I am trying to run the CG version using VOTCA.

I want to coarse-grain the the two carbons in the backbone into one bead, the carbonyl-amide group into another bead, and the isopropyl group into 3 distinct beads as shown in the picture below.
My question is, if I have a 40-monomer long chain, does my .xml file need to have definitions for 40x3=120 beads? Is there a way around this?

Unfortunately not, but you could write a little python script to generate the xml mapping file for you.

Christoph

I ask this out of curiosity. If there is no way around this, I will for sure be writing some scripts to help with the process.

Thank you for any advice you have for me! :)

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