Re: 2.7b metadynamics ::hBond component :: folding of a single helix in water

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Mon Jun 22 2009 - 15:18:52 CDT

Hi Ali, in the hBond variable "acceptor" and "donor" are individual
atoms, not groups: the values for those keywords are simply the atom
indexes.

Metadynamics by default uses grid to cache the hills: if you don't
want to set boundaries, set useGrids to "no" inside metadynamics, and
all gaussian hills will be computed individually at every time step
(the "traditional" way).

Ciao
Giacomo

---- ----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
 phone: (+1)-215-573-4773
 fax: (+1)-215-573-6233
 mobile: (+1)-267-324-7676
 mail: giacomo.fiorin_<at>_gmail.com
 web: http://www.cmm.upenn.edu/
---- ----

On Mon, Jun 22, 2009 at 3:23 PM, Ali Emileh<ali.emileh_at_gmail.com> wrote:
> Hi Giacomo,
>
> Thanks for all the comments and guidance.
> I never saw a negative value of the colvars in the simulation, just the
> boundaries in the
> log file and it got me worried, but I think the core of the colvars module
> is working
> just fine and producing alpha values of the right sign.
>
> I thought I can forget about the alpha component and use a combination of
> dihedrals and
> hBond/distances to fold the helix for now. I started with a simple config
> like this :
>
> =====================
> colvarsTrajFrequency 1000
>
> colvar {
> name hb
> outputAppliedForce on
>
> hBond {
>
> acceptor {
> atomNameResidueRange O 100-105
> psfSegID G
> }
> donor {
> atomNameResidueRange N 106-110
> psfSegID G
> }
>
> }
> }
>
> metadynamics {
> colvars hb
> hillWeight 0.04
> dumpFreeEnergyFile yes
> }
> =====================
>
> I know it lacks boundaries. I just wanted to get the thing to work in steps.
> But the problem
> is I can't get it to recognize the colvar components. It gives me the erro :
>
> colvars: Error: in parsing "acceptor".
> colvars: If this error message is unclear, try recompile with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> now when I change the component from hBond to coordnum and the atom groups
> to
> group1 and group2 (I can't get it to accept any group name other than these,
> reports
> that "Error: definition for atom group "group1" not found."), it goes
> through the component
> recognition and parsing (at least it seems to do so) and gets stuck in the
> "colvars: Tried
> to initialize a count grid on variable with undefined boundaries" error
> message which can
> be fixed by defining boundaries (I DOES go into the simulation). So all I
> can conclude
> here is that I'm missing something in the atom groups definition.
>
> Any thoughts on this will be highly appreciated.
>
> Thank you,
> Ali
>
> On Wed, Jun 10, 2009 at 9:57 AM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>
> wrote:
>>
>> Hi Ali, I see: what you mean (narrowing a1 to an interval of interest) is
>> a
>> good idea, but to do so you also need to set some force constants at
>> the two boundaries. Otherwise, those are just the limits of the grid, and
>> they get expanded over time as the colvar moves outside of them. The
>> fact that lowerBoundary goes negative can be worrisome, but it is only
>> due to the
>> fact that the code managing the grid doesn't know that a1 can't go
>> negative, and allocates a buffer region.
>>
>> Of course, it's never 100% guaranteed that the code is free of bugs,
>> especially at this stage. So, if you do observe negative values of
>> the alpha variable in the .colvars.traj file, I'd like to know.
>>
>> You're applying small hills (0.04 kcal/mol) but very frequently (10
>> steps), so you *are* pumping energy into it. Maybe the helix is just
>> too stiff and by the time you've added energy to one structure
>> metadynamics has moved it back to a similar one?
>>
>> This is why I suggest that you try the harmonic steering: you could,
>> say, set a target of 1 to try and fold the helix completely. Unlike
>> in metadynamics, at least you'd drive it monotonically there, and
>> you'd have to cope with less complications.
>>
>> Otherwise, if your target is the folded helix, and the other
>> structures are not relevant to you, it may simply be happening that
>> because of the system's nature the colvar does not respond as quickly
>> as you want it to, because other degrees of freedom need to be forced
>> (i.e. additional colvars).
>>
>> Ciao
>> Giacomo
>>
>> ---- ----
>> Giacomo Fiorin
>> Center for Molecular Modeling at
>> University of Pennsylvania
>> 231 S 34th Street, Philadelphia, PA 19104-6323
>> phone: (+1)-215-573-4773
>> fax: (+1)-215-573-6233
>> mobile: (+1)-267-324-7676
>> mail: giacomo.fiorin_<at>_gmail.com
>> web: http://www.cmm.upenn.edu/
>> ---- ----
>>
>
>

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