Re: Rotate two linked proteins against each other and calculate energy profile

From: Bjoern Olausson (
Date: Sun Mar 20 2011 - 11:03:32 CDT

Thanks again for your suggestion Ajasja, I am still planing the setup
and I finally decided to go with "colvars" and "SMD".

I am mulling over your "colvars" and Dihedral suggestion.
Since it is the first time I am using "colvars" I am somewhat
uncertain how I should group the atoms.

My current Idea to define a dihedral would be the following:
Group 1: Monomer A
Group 2: First half of the linker
Group 3: Second half of the linker
Group 4: Monomer B

Does this make sens to you?

To come back to the Ethan molecule, Group 1 would resemble a Proton on
C1, Group 2 would be C1 itself, Group 3 would be C2 and Group 4 would
be a Proton on C2.

Is this analogy correct?

Finally I would apply a force to Monomer A (Group 1) to rotate it
(maybe I have to constrain Monomer B, but we will see)

Does this sound reasonable?

Thanks a lost for your suggestions,

On Tue, Mar 15, 2011 at 22:56, Ajasja Ljubetič
<> wrote:
> Hi,
> Perhaps the colvars module would be of interest to you as well. You could
> define a dihedral colvar between the two subunits and obtain the free enrgy
> profile of the rotation.
> Best regards,
> Ajasja
> On Tue, Mar 15, 2011 at 20:20, Bjoern Olausson <>
> wrote:
>> Hi NAMD users,
>> I have a homo dimer which is linked via a short peptide linker. The
>> two monomers are supposed to rotate more or less free against each
>> other.
>> I would like to follow the energy profile while one monomer is rotated
>> 180 degrees to see if there is on favorite position. Something like
>> the energy profile when rotating the dihedral angle of an Ethane
>> molecule.
>> I already have a explicite solvent, all-atom simulation running for this
>> system.
>> Now my qestions:
>> a) Would I use FEP for the energy profile (Use coordinates from my
>> simulation as start structure and as target structure take coordinates
>> from a SMD run where I rotate one monomer by 180 degrees)? I guess
>> not. Since I can't tell FEP where to go.
>> b) Instead of using FEP,  is it possible to just run a SMD where I
>> rotate (rotConstraints) one monomer by 180 degree and calculate the
>> forces from the SMD output (like in the NAMD tutorial "Force Analysis
>> for Constant Velocity Pulling"
>> c) Is it possible to rotate a molecule using tcl forces instead of SMD?
>> Thanks for you help.
>> Cheers,
>> Bjoern

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