[gmx-users] AFM pulling of two groups
gmx3 at hotmail.com
Wed Jan 19 16:54:06 CET 2005
>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
>I'm trying to use AFM pulling to prepare my starting structure (with
>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
You did not supply the force constants for the afm pulling (afm_k1 and
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.
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