[gmx-users] Constraints - again

Uwe Richter 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 
applied position
restraints. To these atoms I defined distance restraints for my real 
atoms, however,
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 
easier way
to do it?

Thanks again,

David van der Spoel wrote:

>On Wed, 2004-12-15 at 12:53 +0100, Uwe Richter wrote:
>>Dear all,
>>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
>>Please don't post (un)subscribe requests to the list. Use the 
>>www interface or send it to gmx-users-request at gromacs.org.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20041216/0fb0e1f8/attachment.html>

More information about the gromacs.org_gmx-users mailing list