[gmx-users] AFM pulling of two groups

[Berk Hess]

>From: Ester Chiessi <ester.chiessi at uniroma2.it>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: [gmx-users] AFM pulling of two groups
>Date: Wed, 19 Jan 2005 14:20:00 +0100
>
>Hi all.
>
>I'm trying to use AFM pulling to prepare my starting structure (with
>Gromacs 3.2.1).
>After a fail in working with the reference group left blank ( is it a bug?)
>I tried to pull simoultaneously two groups relative to the reference group.
>
>I can't understand why, but it seems that pulling is only on the group_1,
>although I give also a group_2.

Pulling is always between the reference group and one or more other groups.
If you want to pull between two group you need to supply the reference group
and group_1.

You did not supply the force constants for the afm pulling (afm_k1 and 
afm_k2).
Maybe afm_k2=0.
It's all descibed in the pdf manual.

>
>There is also a strange thing: the first element of the group seems to have
>an atom number reduced of a unity ( i.e. 144 instead of 145 ) and the index
>file is correct.

In the code the atom numbering starts at 0.
The person who implemented this forgot to add 1 in the print statement.

Berk.

_________________________________________________________________
Play online games with your friends with MSN Messenger 
http://messenger.msn.nl/