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3 votes
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Does GROMACS have the capability to do Monte Carlo simulation of proteins?

GROMACS does not support "pure MC" calculations, but it uses MC algorithms for many things. According to the GROMACS mailing list, there is a very old version (pre-2016) which has a plug-in ...
Bdrs's user avatar
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4 votes
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Restrain a protein to be helical in an MD simulation

The general method is to constrain the CA atoms of the protein while you are equilibrating the structure. You can do this in gromacs by creating a posres.itp file that has all the CA atoms, and then ...
Hemanth Haridas's user avatar
5 votes

Restrain a protein to be helical in an MD simulation

Applying restraints to keep a specific secondary structure is common/mandatory when using coarse grained force fields for MD simulations, try searching for simulations with the MARTINI force field.
Frank Jensen's user avatar
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