[gmx-users] Trajectory guided by density maps

[Ramon Guixà]

Hi Christian,

Ok, so If can't apply forces from two density maps at the same time then I
don't see how can I perform a guided transition.
I mean, I figured I would need to gradually switch on one map while
switching off the other, but for this I need to apply both restraints at
the same time right?

Do you see another way of doing this?

Best,
Ramon

On Thu, Dec 12, 2019 at 12:23 PM Christian Blau <blau at kth.se> wrote:

> Hi Ramon,
>
>
> This feature will be released in January ;) and is in a beta version, soon
> to be release candidate, so you are
> definitely an early adopter.
>
> Most of the parameters are set by default in the .mdp file if you do not
> set them yourself, you'll see them also in
>
> http://manual.gromacs.org/2020-beta3/user-guide/mdp-options.html
>
>
> It is hard to give very general advice on the parameters, but some things
> to observe:
>
>   - the force constant can have a very large range of values, try changing
> the order of magnitude first, if you don't
> have an idea, or try "adaptive force scaling"
>
>   - the resolution parameter
> density-guided-simulation-gaussian-transform-spreading-width is important
> as well and
> interplays with the force-constant - if this value is high (low
> resolution), the forces will go down as well (there is
> not so much force needed to make a blob be similar to anything)
>
>   - density-guided-simulation-nst may be crucial for performance, the
> blobbier the densities and / or previous value the
> larger you can set this value. 20 or so is a good first guess for lots of
> applications
>
>
> For now you cannot apply forces from two density maps at the same time,
> though this is an obvious possible extension for
> a next release.
>
> Since I just implemented the feature, I'll be interested in how things
> work out for you and what is yet unclear in
> documentation, etc..
>
>
> Best,
>
> Christian
>
>
> On 2019-12-12 11:58, Ramon Guixà wrote:
> > 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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