Re: How to "twist" a molecule? (resubmit)

From: Victor Ovchinnikov (ovchinnv_at_mit.edu)
Date: Mon Jun 11 2007 - 20:21:35 CDT

Hi, Margaret.

Just a thought. In the file SimParameters.C, the following code turns
all constraints off if 'constraints' is undefined:
Do you have "constraints on" elsewhere in your input file?

Victor

////////////////////
 if (!opts.defined("constraints"))
   {
     constraintExp = 0;
     constraintScaling = 1.0;

     //****** BEGIN selective restraints (X,Y,Z) changes
     selectConstraintsOn = FALSE;
     //****** END selective restraints (X,Y,Z) changes
 
     //****** BEGIN moving constraints changes
     movingConstraintsOn = FALSE;
     //****** END moving constraints changes
     //****** BEGIN rotating constraints changes
     rotConstraintsOn = FALSE;
    //****** END rotating constraints changes
   }
   //****** BEGIN rotating constraints changes
   else {
     if (rotConstraintsOn) {
       rotConsAxis = rotConsAxis.unit();
     }
   }
.
.
.
//////////////////////////////////////////////////////

On Mon, 2007-06-11 at 18:49 -0400, Margaret S. Cheung wrote:
> Hi All,
>
> I think I will need to revisit this problem, because I just realized
> that NAMD program is not rotating the molecule even though the
> configuration file was set so.
>
> My configuration file
>
> rotConstraints on
> rotConsAxis x y z
> rotConsPivot x y z
> rotConsVel xx
>
> But in the log file, it gave me warning as
>
> Warning: The following variables were set in the configuration file but
> were not needed.
> Warning: rotConstraints
> ....
>
> And I tried to see if rotConsPivot is in the log file, and they are not!
> Does it mean that my NAMD program is not rotating the molecule?
>
> Please help!
> Sincerely,
> Margaret
>
>
> Grzegorz Jezierski wrote:
> > Dear Margaret,
> > Now I think I understand your problem.
> > As mentioned on p.71 of NAMD manual, Rotating Constraints are set up
> > the way ordinary (i.e. positional) restraints are.
> > In my example, reference positions for Rotating Constraints are
> > specified in R6G_6CAA.pdb file, and force constants are specified in
> > fixed.pdb file, in 10th column.
> > A line in my fixed.pdb file which specifies the force constant for
> > Rotating Constraints looks like this:
> > ATOM 46 O1 MOL 2 -0.300 -1.495 2.119 0.00 1.00
> > If I put e.g. 0.00 instead of 1.00, the Rotating Constraints option
> > for this atom will be switched off.
> > Now in order to combine his with harmonic restraints, include your
> > desired restraint definition in a separate file (pmf.conf in my
> > example); description on p.82, use 'mcti' keyword. Specify
> > 'freeEnergy on'. I used this option for constraining a system, not
> > just for free energy calculations.
> > Alternatively, you may want to specify 'fixed atoms'. This seems like
> > a more suitable option for your study. In this case, you should use a
> > different column (e.g. 'O' i.e. 9th) in the pdb file.
> > Hope this helps
> >
> > Margaret S. Cheung wrote:
> >> Hello,
> >>
> >> I tried with both rotational and harmonic contraints, but now I see
> >> the possible problem JC mentioned.
> >>
> >> The question is "how to set reference positions for rotating
> >> constraints"? The manual simply said that the rotational constraints
> >> parameters are specified in the same manner as for usual
> >> (static)harmonic constraints". I assume it means that we need to set
> >> consref, conskfile, conskcol for the harmonic constraints.
> >>
> >> But if I now included rotational constraints to harmonic one, how can
> >> I set the reference positions for rotation since all it has is
> >> rotConsAxis, rotConsPivot and rotConsVel?
> >> When I set constraints on, did it mean "all atoms" in the system will
> >> be rotated? Can I apply rotation (twist) to only a part of the
> >> molecules (e.g. excluding water molecules)?
> >> Thank you.
> >> Sincerely,
> >> Margaret
> >>
> >> Grzegorz Jezierski wrote:
> >>> I've run simulations with almost any combination of Rotating
> >>> Constraints, Harmonic Constraints, Fixed Atoms and PMF constraints.
> >>> Here is a relevant part of one of my input files:
> >>>
> >>> Constraints on
> >>> consRef R6G_6CAA.pdb
> >>> consKFile fixed.pdb
> >>> consKCol B
> >>>
> >>> rotConstraints on
> >>> rotConsAxis 3.50 4.15 -20.45
> >>> rotConsPivot 3.50 4.15 -24.37
> >>> rotConsVel 0.0030
> >>> freeEnergy on
> >>> freeEnergyConfig pmf.conf
> >>>
> >>>
> >>> Regards,
> >>> Greg
> >>>
> >>>
> >>> On Sun, 25 Mar 2007, JC Gumbart wrote:
> >>>
> >>>
> >>>> Your suggestion definitely sounds like it might work (using
> >>>> fixedAtoms that
> >>>> is); you can't use harmonic constraints and rotating constraints at
> >>>> the same
> >>>> time though, if I understand the manual correctly. I haven't seen
> >>>> rotatingConstraints used by anyone myself, so you may just need to
> >>>> experiment
> >>>> with it. You could also try using IMD to control the forces
> >>>> interactively.
> >>>> Let us know how it goes.
> >>>>
> >>>>
> >>>> On Mar 23, 2007, at 11:05 AM, Margaret S. Cheung wrote:
> >>>>
> >>>>
> >>>>> (I apologize if you are reading this message again. The previous
> >>>>> one perhaps
> >>>>> was
> >>>>> bounced because I haven't registered my current email address to
> >>>>> NAMD-L, as
> >>>>> warned
> >>>>> by NAMD-L regulators)
> >>>>>
> >>>>> Hi NAMD users and developers,
> >>>>>
> >>>>> I'd like to "twist" a molecule by applying a torque along an axis.
> >>>>> I am
> >>>>> looking at "rotating constraints" in the user guide. But a simple
> >>>>> rotation
> >>>>> is not what I want. Somehow I would want to "fix" a few distant
> >>>>> atoms away
> >>>>> from the pivot point so that the molecules can be twisted
> >>>>> eventually (ex:
> >>>>> like winding up a helical structure). If so, would you recommend
> >>>>> including
> >>>>> "harmonic constraints" or simply assigning a few "fixed" atoms to the
> >>>>> reference pdb file in order to accomplish that? Please advise and
> >>>>> thank you
> >>>>> for your time.
> >>>>>
> >>>>> Margaret S. Cheung
> >>>>> Assistant Professor
> >>>>> Department of Physics
> >>>>> 629C Science and Research 1
> >>>>> University of Houston
> >>>>> Houston, TX 77204-5005
> >>>>> email: mscheung_at_uh.edu
> >>>>> (O)713-743-8358 (F)713-743-3589
> >>>>> http://thoth.phys.uh.edu/~mscheung/
> >>>>>
> >>>>
> >>>
> >>>
> >>
> >
> >
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:49 CST