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I have a very small part of a protein that is supposed to be helical. However, in molecular dynamics simulation, it unfolds and gets into extended conformation. Is there any way I can force it to stay helical by applying any restraints, or any other biases? Thanks.

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  • $\begingroup$ Thanks a lot for the edit :-D $\endgroup$ Commented Mar 27 at 9:06
  • $\begingroup$ Did any of the provided answers sufficiently clarify your query? If yes, mark that answer as accepted. $\endgroup$ Commented Apr 3 at 15:39
  • $\begingroup$ Thanks a lot to everyone for the answers. Adding to what Hemanth suggested, having a distance restraint between two atoms at the end of the helix along with the atoms that take part in the hydrogen bonding in the helix kept my starting helical structure helical. To answer to leading unphysical simulation, this is exactly what I wanted to perform :-) This is the case study I wanted to study, not to reproduce anything ;-) Simulations can indeed be used as a nice toy model tool to study some unphysical things. Thanks $\endgroup$ Commented Apr 5 at 15:00

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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 having restraints turned on in the mdp file.

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  • $\begingroup$ Thanks Hemanth. I did the same, but during the production run, after the restraints were removed, the structure was no longer alpha-helix. $\endgroup$ Commented Mar 27 at 15:54
  • $\begingroup$ You can also use a harmonic restraint to ensure that the structure remains an alpha-helix. You might need to use collars to specify that the end to end distance of the residues must remain within some distance. $\endgroup$ Commented Mar 27 at 15:59
  • $\begingroup$ Can you elaborate more on these harmonic restraints? What kind of harmonic restraints - like distance, angle? $\endgroup$ Commented Mar 27 at 18:16
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    $\begingroup$ You can use a distance restraint to keep the ends of the helix at a fixed distance, meaning that they will no longer melt away to a different structure. $\endgroup$ Commented Mar 27 at 20:41
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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.

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  • $\begingroup$ Thanks a lot, Frank. But, it's an all-atom structure, not a CG one. $\endgroup$ Commented Mar 27 at 10:49
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    $\begingroup$ You should be able to use the same technique for restraining key backbone atoms in an all-atom force field. $\endgroup$ Commented Mar 28 at 12:04

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