VMD-L Mailing List

From: Negar Ashari Astani (negarastani_at_gmail.com)
Date: Tue Sep 01 2009 - 11:58:32 CDT

Hi VMD experts

My system consists of two walls and 3000 particles between them, I have
inserted water molecules with GROMACS into my box and some of them are
located behind my walls, Water molecules with z value more than 30 nm are
outside the walls and should be omitted. I wrote the script below for this
purpose but the output file is empty, I would be so grateful if i could have
your comments on its problem:

mol delete all
set sys [mol new input.pdb]
set wal [atomselect $sys "resname WAL and name WL"]
set walminmax [measure minmax $wal]
set wal_maxz [lindex $walminmax 1 2]
set outwat [atomselect $sys "resname SOL and name OW and z >
$wal_maxz" ]
set watminmax [measure minmax $outwat]
set outwat_id [$outwat get resid]
set finalsys [atomselect $sys "all and not resid $outwat_id"]
$finalsys writepdb out1.pdb 

-- 
Negar Ashari Astani