Re: Special constraint on MD simulation

From: Jérôme Hénin (
Date: Mon Aug 05 2013 - 12:46:05 CDT

Hi Carlos,

You can use the Collective Variables to apply an RMSD restraint on the alpha carbons of the protein.

See an example there (you only need the RMSD variable, not the two others):

and of course the user's guide:


----- Original Message -----
> Hi you all,
> I want to perform a MD simulation of a protein with water as solvent
> and near to a POPC membrane.
> The thing i want to see is how the protein can get through the
> membrane and at the same time can interact with both, the head
> groups and the fatty acids of it.
> My problem is that, i want to maintain also the secondary structure
> of the protein, but if i put a value of constraint the protein will
> not move of its initial position.
> So, in other words.
> Is there a way to use an specific constraint on the protein that can
> allow it to maintain its secondary structure, but at the same time
> can allow it to move through all the system? (including the POPC
> membrane, of course)
> Hope someone can help me with this.
> Thanks in advances,
> Carlos
> ps- sorry for my bad english
> --
> Carlos Navarrro Retamal
> Sent with Sparrow

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