[gmx-users] Trajectory guided by density maps

[Christian Blau]

Hi Ramon,


This is definitely a way to obtain a transition path.

One things to consider here is that you deliberately "throw away" already perfect information about your target 
structure, so it might be harder to reach. On the other hand you might not care to have an exact overlap with the 
structures, so in this sense using the density might aid you in finding a more realistic transition path that is closer 
to the lowest free energy barrier. If you're interested in that, using very low resolution maps might even be beneficial.

I personally would be excited to hear about your findings.

Best,

Christian


On 2019-12-11 17:18, Ramon Guixà wrote:
> Hi there,
>
> I would like to use GROMACS to create a trajectory that goes from one
> crystal structure to another crystal structure, both obtained from the same
> system using time resolved crystallography.
>
> Would it be feasible to use the newly implemented density-guided
> simulations parameters to guide this simulation by first fitting the
> initial crystal structure its density map and then switching off these
> restraints while switching on the density map restraints of the second
> crystal structure? I figured this would in principle create a trajectory
> that better reflect the transition from one state to the other, but I am
> not even sure if this makes sense at all...
>
> Thanks in advance for the guidance,
> Ramon