[gmx-users] Trajectory guided by density maps

[Ramon Guixà]

Hi Christian,

I see, ok. Thanks a lot for your feedback, really helpful!

Best,
Ramon

On Thu, Dec 12, 2019 at 1:22 PM Christian Blau <blau at kth.se> wrote:

> Hi Ramon,
>
>
> You would not need to keep your system constrained in the state that you
> started from to see a transition. Pushing state
> A , based on a crystal structure, into state B , described by a density,
> should give you just the transition you want.
>
> If you would like to choose an arbitrary point "between" the two states,
> however, you would have to use maps of both states.
>
>
> Best,
>
> Christian
>
> On 2019-12-12 12:37, Ramon Guixà wrote:
> > 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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