VMD-L Mailing List

From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Thu Oct 04 2007 - 13:34:16 CDT

Hello,
recently with the help of Peter, I used this script to do NAMDENERGY
analysis of my simulated trajectory and it worked fine (almost).
My system details: waterbox of 15 Ang from the surface of protein (segname
PTO1) containing other protein and ions also. And my aim is to calculate VDW
interaction energies between segname PTO1 with its surroundings (to do
binding free energy analysis)
.............................................................................................................................................................................
package require namdenergy
set sel1 [atomselect top "segname PTO1"]
set sel2 [atomselect top "(within 15 of segname PTO1) and not segname PTO1"]
for {set i 0} {$i < [molinfo top get numframes]} {incr i} {
$sel1 frame 0
$sel2 frame 0
namdenergy -sel $sel1 $sel2 -vdw -skip [molinfo top get numframes] -par
par_all27_prot_na.prm -extsys x.xsc -ofile elect1-$i.dat -switch 10 -cutoff
12
animate delete end 0
}
...........................................................................................................................................................................
Now i have some doubts and i was wondering if someone can again help me out
please:
1) when I changed the set sel2 (line 3) in this script from
"(within 15 of segname PTO1) and not segname PTO1"
to
"(within 20 of segname PTO1) and not segname PTO1"
the output of VDW energies changed drastically, which is the way it should
behave, but what i don't understand is that later in the script i am
specifying the switch and cutoff distance (10 and 12 Ang.) which are both
smaller thn the selected values in line 2 so why should there be any
difference in the output VDW energies (i.e. it shouldn't matter what lies
beyond 12 Ang. cutoff).

2) Also from this script, in the output i get only half the number of VDW
energies, compared to the number of frames i have in my dcd file (i.e.
"molinfo top get numframes" is 100 but i only get 50 VDW values in my
output)!!

I would greatly appreciate any input form the members.
thank you
narender