[gmx-users] constraint/restrain distance
gmx3 at hotmail.com
Thu Aug 26 17:10:08 CEST 2004
>From: ÿffffc1ngel Piÿfffff1eiro <anxomx at yahoo.es>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] constraint/restrain distance
>Date: Fri, 20 Aug 2004 14:39:52 +0200 (CEST)
>Dear gromacs users,
>I want to calculate the force to fix the distance
>between two molecules A and B. I think that it is not
>possible at the moment to restraint the distance
>between different molecules in the topology, so I
>tried to use the pull code. I started to play with the
>3 different options (AFM, CF and umbrella sampling)
>but I found several problems.
The crashes in constraint pulling could be due to the short distance.
As I understood the two small molecules are at short distance.
The constraint could introduce a high stiffness into your system
such that with some conformations of the two molecules the forces
get too high.
As for AFM and umbrella pulling.
It would be nice to use these for this purpose.
But they have been implemented with a different purpose.
The problem is that the distance between the group and the reference
is set with a vector, not with a distance.
So you can restrain the vector between the centers of mass of the two
to (0.3,0,0) by setting:
pulldim = Y Y Y
pos1/afm_init1 = 0.3 0 0
Using pulldim = Y N N leaves the molecules free to move in the y and z dir.
It might be better to change the afm and umbrella options to the way
the constaint option works, with a direction that can be zero
so you can restrain the distance and not to a vector.
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