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

[Giuseppe Léonardo Licari]

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