VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri May 04 2007 - 13:23:48 CDT

Hi Lan,
the error you're getting means that namdenergy can't find your namd2
binary. It looks first in /usr/local/bin/namd2; failing that, if you're
using the gui version, it will pop up a dialogue box asking you to
locate your namd binary. I don't yet have a text mode equivalent for
this; I'll add it to my to-do list. In the meantime, you may want to try
using the gui version instead (this will mark the first and only time
anyone ever hears me advocating a gui over a text interface ;-).

What I mean by that remark you link is that if you have some particular
function you want to calculate, the fallback method to do it is just to
write a tcl script that calculates what you want. If you wanted to
calculate the energy of a hydrogen bond as f(x) for any f, for example,
you could write a loop over all the frames that ran measure hbonds, made
selections to get the coordinates of the atoms involved in hydrogen
bonds, and then apply f to them and collect the results. I meant this as
a last ditch method for calculating some characteristic when no
pre-existing tool does what you want, but it highlights the versatility
of having a scripting interface, because there is at least some way to
calculate whatever quantity you might be after with a little work.

Peter

lanhua wrote:
> Hi,
> I had one problem when I tried to calculate the non-bond interaction between two atom selections by using the following command in the text interface:
> >set sel1 [atomselect top "protein and name HN"]
> >set sel2 [atomselect top "water and name OH2"]
> >$sel1 frame 0
> >$sel2 frame 0
> >namdenergy -nonb -sel $sel1 $sel2 -switch 10 -cutoff 12 -skip 5 -extsys namd-temp.xsc -pme
> (Where namd-temp.xsc was generated by clicking "Generate" on the NAMDEnergy GUI)
> I was told that "couldn't execute "": no such file or directory". Could you please tell me how to figure it out?
>
> In addition, I am confused about what Peter said here (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8483.html) about "or write your own script to take the coordinates in vmd and run them through an arbitrary energy function over the trajectory. "
>
> Thanks a lot!
>
> Best regards,
> Lan
>
>
>