[gmx-users] Selection of molecule close to interface in trajectory

[Mark Abraham]

Hi,

The syntax in gmx select is amply capable of expressing pretty much your
exact command, and well documented with it's own online help, also
reproduced here
http://manual.gromacs.org/documentation/5.1.2/onlinehelp/selections.html.
Since you're surely gong to want to change any suggestion someone might
make, you're still going to want to understand what your options are :-)

Mark

On Wed, Jul 6, 2016 at 1:20 PM Giuseppe Léonardo Licari <
Giuseppe.Licari at unige.ch> wrote:

> Dear all,
> I have a simulation where a dye is interacting with a phospholipid
> interface. Sometime the dye is adsorbed, sometimes not. I use a selection
> expression in VMD to select the dye when it is adsorbed at the interface,
> something like:
>     "same residue as((within 3 of resname DPPG) and (resname TSBZ) and
> z>50)"
> where DPPG is the phospholipid and TSBZ is the dye. But saving the pdb
> file of this selection gives an empty file (I guess because some frame
> contains no atoms in the selection). Is there a way to do the same
> selection and save a pdb file with all the adsprbed dye structures using
> some tool in Gromacs (like gmx select)? If so could you please suggest me
> the expression on the basis of the reported VMD example?
>
> I appreciate your help and wish you a nice day.
> Regards,
> Giuseppe
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