I'd like to know where to start with to simulate a gel phase. Force field (I've seen that COMPASS is usually employed), what's the difference in terms of parameters with respect the usual simulation in solution, protocols or tutorials available, etc.
I've found a few articles on md simulations of hydrogel systems but they don't include a detailed description on the setup of the hydrogel model.
I'd appreciate your comments.
Force Fields for carbohydrates are still under development. You must be carefull as you use those existing force fields
Hello superiors, I have seen the following link
http://cms.mpi.univie.ac.at/wiki/index.php/MDALGO
But can you guys please help me how to decide the initial choices of LANGEVIN_GAMMA, LANGEVIN_GAMMA_L, PMASS parameters ??
How these parameters varies from atom to atom ?
Which version of VASP is capable of doing these ?
Thanks,
chanchal
Hi Andre S Pimentel. I'm not sure that I can agree with that. The first GLYCAM force field was developed more than a decade ago and since then the improvements have been very significant, not just for simple sugars but, recently, also for highly substituted ones like sulphated GAGs. I can agree that we have to be careful, or even avoid, using non-carbohydrate specific force fields to model glycans, but as long as you use the right set of parameters, the validation with the experimental data es quite good in general terms. Please see an example here https://www.ncbi.nlm.nih.gov/pubmed/23903025
Dear Majid,
thank you for your comment, but I was asking for specific tools/parameters, if any, to model a carbohydrate network in gel phase. The paper you attached doesn't mention gels in particular, but thank you anyway.
I have experience on MD simulations of water solvated carbohydrate systems, but as a gel contains both the mobile nature of liquids a some of the rigid nature of solids I was just wondering if there are any protocols developed on how to parametrise/scale the potential energy terms of a gel simulation to take this into account.
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