VMD-L Mailing List

From: Lan Hua (lan.hua_at_gmail.com)
Date: Wed Mar 17 2010 - 21:18:55 CDT

Hi everyone,

     I want to test how sensitive the electrostatic interaction energy
between one solvent molecule and the rest of system is to the cutoffs
without using pme. The text command I used is something like as follows:

    set sel1 [atomselect top "residue 100"]
    set sel2 [atomselect top "not residue 100"]
    set cutofflist [list 8 10 12 20 80]
    foreach cutoff $cutofflist {
    namdenergy -elec -vdw -sel $sel1 $sel2 -cutoff $cutoff -switch [expr
{$cutoff-2}] -extsys test.xsc -exe ./namd2
   }

   The vdw interaction energy decrease slightly with the increase of the
cutoff, while the electrostatic energy increase with the increase of the
cutoff, which does not make sense. Any suggestions? Thank you so much!

Best,
Lan Hua