I would like to calculate the characteristic rotation time of a protein domain in its folded state. Under the conditions I'm simulating the protein is near its midpoint of stability, therefore within a single simulation trajectory conformational exchange between folded and unfolded states occur. This means it can be difficult to calculate the characteristic rotation time of the folded state only (especially if conformational exchange is faster than or equal to rotation time scale).
To get around this conformational exchange issue, and calculate the rotation time scale of the folded domain alone, I've applied a harmonic restraint (see below) to keep the domain folded near its crystal structure. My question is, will 'cons harm bestfit' alter the rotational time scales of the folded state? According to cons.doc no torque is added to the restrained system with the bestfit option.
I also recognize that fluctuations in the folded ensemble may be altered, but I imagine this will have only a marginal effect on the overall rotational time scale of the folded state.
Here is the command I use.
cons harm bestfit mass force 5.0 comp sele segid A .and. (resnam G46:G52 .or. resnam G61:G64 .or. resnam G69:G75 .or. resnam G80:G88) end
Any comments would be appreciated.