Hi,
I have a 2-domain protein connected by a 28 residue linker. From experimental data, we know there is very little changes with each of these domain however our hypothesis is that the linker connecting these two domains undergo large confirmation change.
What we would like to do is to perform a simulation by treating the two domains as rigid body (allowing them to move as one unit) and simulate the confirmations of the linker.
Would it be possible to do this either in GROMACS or NAMD ?
Thanks,
Nitish.
I think you can use freezegroup of gromacs. But freezegroup can not fully hold rigid body.
Isn't freeze group used to fix the position of an atom ? I am looking at treating the section as a rigid body which can move in a relative manner to the linker but just not undergo large confirmational changes.
If you are familiar with CHARMM program, you may be able to achieve what you are asking. You can have a look at the following link for a documentation:
https://www.charmm.org/charmm/documentation/by-version/c41b1/params/doc/mc/
You can freeze the groups by freezegroups ib gromacs or by restraining it.
It seems to me that freeze groups are not what's needed here since the OP still wants the domains to move with respect to another. Why not simply increase the force constant of the dihedral potentials? That should do the trick or at the very least strongly limit conformational changes. You'll need to edit by hand the topology files (.top or .itp in Gromacs) to achieve that though.
NAMD has contraints (a harmonic restorative force back to the equilibrium position) and restraints (fixing atoms). see here. An example is here.
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html
http://www.ub.edu/cbdd/?q=content/using-namd-harmonic-restraints
I have the same question . I use "freezegrps" to treat a group as a rigid body and "freezedim" to ensure the group move in X ,Y ,or Z in gromacs when I undergo MD.
But when I calculate the RMSD of the group , I find the values are large so I don't know how to do. I want to know how you solve the problems. Thanks.
I assume you know the structure of these two static domains? If so, I would get a random set of CA-CA pairs from each domain and measure their distances. I would then run your simulation with all of these distances inside of single harmonic collective variable (colvar). This way the domains have some flexibility but are still held in the same overall structure. The key is to pick the minimum number of distances and colvar constant that holds the experimental structure.
In gromacs you can use command genrestr with proper index you can make position restrain then you need to use flag "define = -DPOSRES option in the .mdp file".
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