VMD-L Mailing List

From: Lan Hua (lan.hua_at_gmail.com)
Date: Mon Mar 15 2010 - 18:02:56 CDT

Hi VMD users,

      I have a question about using namdenergy plugin in vmd-1.8.6. I want
to calculate the vdw energy of water in the bulk region with the rest of
system (the system is protein in 8M urea). The text command I used in
script is something as follows:

For each frame of my trajectory (using bigdcd):

    set bulkwat [atomselect top "water not within 6.0 of protein" ]
    $bulkwat update
    set reslist [$bulkwat get residue]
    set res_unique_list [lsort -unique $reslist]
    foreach res $res_unique_list {

         set mysel1 [atomselect top "residue $res"]
         set mysel2 [atomselect top "not residue $res"]

         set outputlist [namdenergy -elec -vdw -sel $mysel1 $mysel2 -cutoff
12 -switch 10 -par par_all27_prot_na_urea.inp -extsys test.xsc -exe
/home/lh2122/tools/NAMD_CVS_Linux-x86_64/namd2 -debug]

         ........
}

   I got some huge positive vdw energy in the outputlist up to 10^8
kcal/(mol Ĺ). Does anyone know what caused this? Your help will be highly
appreciated. Thanks.

Lan