Dear research gate community,
I am trying to simulate a boron nitride nanosheet covalently functionalized with a short chain polymer using charmm36 force field in gromacs. I obtained the str file of polymer from cgenff and obtained its prm and itp file. Later I prepared a n2t file for the system including the nanosheet atoms and polymer atoms( the atom types were defined as per the atom types in itp file ).I was able to generate the topology file but I am doubtful about my approach as I only used atom types and charges and not the whole itp all the parameter like bond angles, dihedrals were automatically generated. It would be great if someone could guide me whether the approach is correct or not and how can i incoporate the itp parameter for the polymer. Any guidance would be of great value. Thank you!
#charmm36 #GROMACS #CGENFF
Hey there, my fellow researcher Aqsa Kamran! Let's dive into your simulation challenge together. Now, I don't hold back, so here's my take:
It's fantastic that you're working on simulating a covalently functionalized boron nitride nanosheet with a polymer. It's a complex system and getting the topology right is crucial. Here's some guidance:
1. **Bonded Parameters**: You've got the itp file for your polymer, which is great. For your polymer's bonded parameters (bond lengths, angles, dihedrals), you can indeed let CHARMM-GUI or CGenFF generate them for you. However, make sure that your force field (CHARMM36 in this case) is compatible with your polymer. Sometimes, the compatibility might require manual adjustments.
2. **Charges**: The charges are a critical aspect. You mentioned you have charges from CGenFF for your polymer, and you're using these charges for your nanosheet as well. This is a reasonable approach if the charges are similar in nature and units (often in partial charges). But be cautious, because nanosheets and polymers might have different charge models. If possible, validate these charges through ab initio calculations or literature data.
3. **Non-bonded Parameters**: Ensure that your itp file for the polymer has the correct non-bonded parameters (Lennard-Jones parameters) for the atoms. These parameters are critical for the interactions between atoms in your system.
4. **Topology Integration**: You might need to manually integrate the itp parameters for your polymer into your system's topology. This means copying the bonded and non-bonded parameters from your polymer itp file into your system topology file. Be careful with atom type naming conventions; they should match between the itp file and the topology.
5. **Testing**: Before you dive into production simulations, always perform a thorough equilibration and validation of your system. This helps you catch any anomalies or issues with your topology.
6. **Consult the Literature**: If possible, look for publications or literature data that have dealt with a similar system. They might provide insights into the force field parameters and topology generation.
Remember, simulation can be a trial-and-error process, and it's essential to validate your results against experimental data or other reliable sources. If you're in doubt about a specific parameter or aspect of your system, it's better to consult with experts in your field or on simulation forums.
I hope this helps you in your simulation journey, my fellow researcher Aqsa Kamran! Don't hesitate to ask me if you need further guidance.
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