[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

[Abhishek Acharya]

Sorry, I forgot to mention one important detail.

I am using gromacs version 2016. I tried gromacs 5.1.2 also; it shows the
same behavior.

Regards,

Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020

On Mon, May 29, 2017 at 1:02 PM, Abhishek Acharya <abhi117acharya at gmail.com>
wrote:

> Dear GROMACS users,
>
> I want to insert my molecule of interest in a simulation box at specific
> positions, specified by a dat file.
>
> Now, when I run insert-molecules, I find that on "certain occasions" (yes,
> it doesn't happen always.), the program also inserts the molecule
> at the origin [0 0 0]. It seems that it is appending the input coordinates
> of my molecule, provided with -ci,
> to the final coordinate file, something which should not happen.
>
> Is this behavior known? Of course, it is trivial to remove the extra
> coordinates, but it becomes an effort if a large number of systems need to
> be
> generated.
>
> Thank you.
>
> Regards,
> Abhishek Acharya
> Research Associate,
> Department of Molecular Nutrition
> CSIR-Central Food Technological Research Institute,
> Mysuru-570020
>