[gmx-users] Constraints - again
urichter at jerini.de
Thu Dec 16 08:46:42 CET 2004
Thanks for the reply,
Distance restraints won't to the job I suppose, since I'd need a second
atom to which
the restraint refers to. I just do not want the atoms of the loop to
move too far from the
current position, say only +/- 2 angstrom in all dimensions. Amber
provides such a
feature but I don't know if it is possible to achieve this with Gromacs.
I have tried to define a set of atoms at exactly the same position as
the loop atoms,
didn't define any bonds, pairs etc. for them, gave them zero charges and
restraints. To these atoms I defined distance restraints for my real
the minimizations/simulations crashed. Is this procedure in general
possible and I
did something wrong in the set up? If not, is there another, may be
to do it?
David van der Spoel wrote:
>On Wed, 2004-12-15 at 12:53 +0100, Uwe Richter wrote:
>>is there a way to let parts of a protein move only a certain
>>distance from the current position. I have a loop and I want
>>to relax it by high temperature MD or simulated annealing but
>>I don't want it to move too far away.
>Use distance restraints (not these are not constraints)
>>Thanks for you help,
>>gmx-users mailing list
>>gmx-users at gromacs.org
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