[gmx-users] Making easy position restrain
Hector Mrz-Seara Monne
hseara at netscape.net
Fri Nov 5 19:44:57 CET 2004
Thanks a lot, it has clarify my problem now everything works, but know I
have problems with a steep of 3fs that without restrains wasn't
present, the system crash after a 1,5 ps. This is normal?
x.periole at chem.rug.nl wrote:
> Hector Martinez-Seara Monne wrote:
>> Hi all,
>> sorry in advance for the question because I'm sure it's not the first
>> time that has been posted but I haven't been able to find it (also
>> the manual gives a short example but not enough for allow me to
>> completely understand how to use it). I just want to know if there's
>> any easy way to define positions restrains over all the atoms of a
>> type instead to number all one by one. If yes can you tell me how?.
>> For example imagine I have a box of SPC water and I want to fix all
>> oxygens ( this is very related with one of the questions I've read
>> today) or I want to fix all the heads of a monolayer in a plane
>> during the equilibration
> From the way position restraint work you have to give a posre.itp file
> to grompp. This file has to contain
> the list of the atom (number) that you want to apply the restrain on
> and its index number. The fact is that
> the restrains have to defined for each molecule type. In the case of
> the water exemple the posre.itp would
> contain the index number of oxygen (3) and the x, y and z restrain
> force (1000 1000 1000 by default).
> You have to define an index (make_ndx) containing the atoms (type if
> you wish) that will feel the restrain
> and give it to genpr -conf.gro -n index to generate the posre.itp
> corresponding to the given molecule. Remember
> that you do not define the position restain based on the conf.gro but
> on the topology of each molecule.
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