VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Oct 04 2007 - 14:18:05 CDT

Hi Narender,
this seems very odd... the only thing I can think of that would cause
this increase is the following: vmd's atomselections do not take
periodic boundary conditions into account, but namd does. Thus, if you
have atoms that are between 15 and 20 angstroms from segname PTO1 when
measured across a periodic boundary, but not within the unit cell, these
atoms will appear in the interactions calculated by namdenergy only with
the longer selection. This is particularly likely to be a problem if
your solvent is not wrapped in your input trajectory (in which case you
should wrap it prior to using namdenergy).

When you say you're only getting 50 outputs, how many output files are
there? 100 separate log files should be generated...

Also, for your case you may find it easier to simply use the gui with
the selections "segname PTO1" and "not segname PTO1" rather than forcing
the selection to update at each time step. In addition, if you only care
about vdw interactions there's no need to turn PME on, as that just
results in extra work.

Best,
Peter

Narender Singh Maan wrote:
> 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
>
>
>