[gmx-users] positional restraint

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 29 15:43:42 CET 2004

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.

> 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
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

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