VMD-L Mailing List

From: Gianluca Lattanzi (gl.lattanzi_at_gmail.com)
Date: Wed Oct 17 2012 - 11:11:09 CDT

Hi, everybody.
I need to duplicate a system I have already equilibrated (POPC
membrane + water and ions). To this end, I wrote a script to obtain
the periodic images of my system and then merge all structures into a
single file. I am unable to generate now a new psf for the big system.
Any help?

I enclose here my script:

package require pbctools
mol load psf ../1M_NaCl.psf namdbin ../1M_NaCl_50ns.restart.coor
pbc readxst ../1M_NaCl_50ns.restart.xsc
set a [molinfo top get a]
set b [molinfo top get b]
set c [molinfo top get c]
set all [atomselect top all]

# Write out the first system
$all writepdb big_sysA.pdb
$all writepsf big_sysA.psf

# Translate by +x and write out new config
$all moveby [list $a 0 0]
$all writepdb big_sysB.pdb
$all writepsf big_sysB.psf

# Translate by -x and +y and write out new config
$all moveby [list [expr {-1*$a}] 0 0]
$all moveby [list 0 $b 0]
$all writepdb big_sysC.pdb
$all writepsf big_sysC.psf

# Translate by +x and write out new config
$all moveby [list $a 0 0]
$all writepdb big_sysD.pdb
$all writepsf big_sysD.psf
$all delete

mol delete all
package require psfgen
resetpsf
foreach S { A B C D } {
readpsf big_sys$S.psf
coordpdb big_sys$S.pdb
}
writepsf big_sys_all.psf
writepdb big_sys_all.pdb

quit 

-- 
Gianluca Lattanzi Ph. D.
Department of Physics
Ph: + 39 080 544 3209 (int. 3209)
University of Bari "Aldo Moro"
Bari, Italy