[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 !
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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