[gmx-users] Trajectory guided by density maps

[Ramon Guixà]

Hi Christian,

thanks a lot for your answer. Good to know this makes sense to someone else
too.
Now I have two questions out of ignorance (never used this newly
implemented feature before):

1) Can I apply two sets of forces (restraints) at the same time, namely one
for each density map?
2) Would you have by any chance an example or a default set of values for
the density-guided options? I am not really sure how to use this feature
anyway...

Thanks!
R

On Thu, Dec 12, 2019 at 11:29 AM Christian Blau <blau at kth.se> wrote:

> 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
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