[gmx-users] about position restraints in optimize

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 19 11:08:55 CEST 2002

On Thu, 2002-09-19 at 10:51, xu yechun wrote:

Dear David,

Maybe I did not express my question clearly.  I use the same em.mdp(list
below) and the same gro file but with the different content of
posre.itp(first time: whole protein; second time: the mainchain of the
protein; last time:only the Calpha of the protein).  The rmsd ( last
step structure to crystal structure) of every  time is identical.  So I
think although I use "define = -DPOSRE" in em.mdp,  the posre.itp is not
be used in optimizing progress, otherwise I should get the different
rmsd of every time. I guess that there is no position restraints in
optimizing process whether using define = -DPOSRE or not.

cpp                 =  /lib/cpp
define              =  -DPOSRE -DFLEX_SPC
If there is a matching position restraint section in your topology it
will be turned on by this. You can check your energies: if there is a
position restraint energy it has been calculated...

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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