[gmx-users] positional restraint

[David]

On Tue, 2004-11-30 at 01:32 +0530, Alok wrote:
> hello David and Xavier,
>                          Thanks for all your responses to my previous
> mails.I am sorry,I still have to bother you with
> some more queries about the constraint.In the
> process i would also like to answer few questions
> u have asked in your responding mails.
> 
> What is the range of differences you observe ?? Is it for the restrained
> part or the rest of the protein ?
> 
> The Observed distance difference is for the restrained part (the atoms
> from the constrained residue).I have not checked the distance difference
> between the other atoms of the protein as i expect it to vary anyway since
> i am constraining only one residue in my protein.
> 
> I present below data of distances (in Angstrom) between atoms of my
> constained residue for the crystal structure as well as for the output
> after Energy minimization using different Force constant.
> 
> 
>                                      (Force Constant)
>          Crystal      1000            10000              100000
>  O-OD1    2.58         3.17            2.87               2.66
Is your OD1 protonated? It should...

>  O-HD21   4.86         5.27            5.13               4.95
>  O-HD22   4.75         5.35            5.06               4.83
>  H-OD1    4.73         4.76            4.75               4.75
>  N-HD21   4.62         4.57            4.74               4.71
>  N-HD22   5.58         5.62            5.65               5.62
>  H-ND2    4.94         4.66            4.80               4.87
> 
> As we can observe even after value of 1000000,the atoms have not freezed
> as u have mentioned in your mail.
> 
> my corresponding ".mdp " file for EM is as follows:
> 
> cpp                 =  /lib/cpp
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  steep
> nsteps              =  10000
> ;
> ;    Energy minimizing stuff
> ;
> emtol               =  200
> emstep              =  0.01
> nstcgsteep          =  1000
> 
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  2.0
> rvdw                =  1.2
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> 
> If I am not able to freeze the atoms even after such high Force Constant,
> then i am going wrong some where as you have suggested.Can you please
> suggest the possible reason for the problem and would be thankfull if you
> can shed some light into the possible solution.
> 
>                                           Thank you,
>                                            Alok Jain
> 
> 
> 
> > David van der Spoel wrote:
> >
> >>On Mon, 2004-11-29 at 15:21 +0100, Xavier Periole wrote:
> >>
> >>
> >>>Alok wrote:
> >>>
> >>>
> >>>>                              Though i have increased the force
> >>>>constant value,I am not sure about the detrimental structural effect (
> >>>>I have read somewher that too large the force constant may result in
> >>>>structural artifacts) it may have on my protein.So I would like to
> >>>>know about the ideal value for the force constant such that the atoms
> >>>>are constrained considerably and also that the protein does not
> >>>>experience any unwanted structural deformation.
> >>>>
> >>>>
> >>>It seems that there is definitely something wrong in your restrains. A
> >>>force constant of 100000 should freeze your atoms
> >>>
> >>>
> >>No! Only if you take a ridiculously small time step, otherwise they will
> >>oscillate into oblivion.
> >>
> >>
> > sorry for expressing myself a bit too fast. Oblivion seems top be much
> > more adapted.
> >
> >>
> >>
> >>>at their original position. If you restrain only a part of your molecule
> >>>it is reasonable to imagine that the rest of the protein
> >>>is responding to "existing" forces.
> >>>A force constant of about 500 to 1000 is ok !
> >>>XAvier
> >>>
> >>>
> >>>
> >>>
> >
> >
> > --
> > ----------------------------------------------
> >
> >    Xavier Periole - Ph.D.
> >
> >    Dept. of Biophysical Chemistry / MD Group
> >    Univ. of Groningen
> >    Nijenborgh 4
> >    9747 AG Groningen
> >    The Netherlands
> >
> >    Tel: +31-503634329
> >    Fax: +31-503634800
> >    email: x.periole at chem.rug.nl
> >    web-page: http://md.chem.rug.nl/~periole
> >
> > ----------------------------------------------
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++