Re: Calculate energy of a residue using NAMD energy

From: Peter Freddolino (
Date: Thu Feb 01 2018 - 22:59:57 CST

In that case, you'd need to use two selections as arguments to -sel, to
specify the two groups that you want to calculate interactions between.
(eg, -sel $watsel $protsel)

On Thu, Feb 1, 2018 at 11:51 PM, Monika Madhavi <>

> Hi Peter,
> Thanks a lot. Yes I was an idiot. I did run with rigid water. What I want
> to calculate is the potential energy of a water molecule at a particular
> distance from a protein (more specifically, at a hydrogen bonding site).
> Best,
> Monika
> On Fri, Feb 2, 2018 at 1:59 PM, Peter Freddolino <>
> wrote:
>> Hi Monika,
>> If you ran with rigid water, and you're just calculating the energy of a
>> single water molecule alone, it ought to be zero. All of the nonbonded
>> interactions are exclusions, and all of the internal interactions are zero
>> by definition.
>> Are you looking for its interaction with the surrounding system? What is
>> the energy that you're trying to calculate?
>> Thanks,
>> Peter
>> On Thu, Feb 1, 2018 at 7:08 PM, Monika Madhavi <>
>> wrote:
>>> Hi Onur,
>>> Thank you very much for your suggestion. Actually it worked. In the
>>> cluster I loaded both NAMD and VMD modules (earlier I had only VMD loaded)
>>> and the script worked.
>>> However, now I have a different problem. As I mentioned earlier, my task
>>> is to calculate the total energy of a water molecule at a particular frame.
>>> So this is the tcl code I used in vmd to do this.
>>> package require namdenergy
>>> set mol [mol new mypsf.psf type psf waitfor all]
>>> mol addfile mydcd.dcd type dcd first 0 last -1 waitfor all molid $mol
>>> set nf [molinfo $mol get numframes]
>>> for {set frm 0} {$frm < $nf} {incr frm} {
>>> set sel [atomselect $mol "index $indo $indh1 $indh2" frame $frm]
>>> set totalE [namdenergy -all -sel $sel -par "myparameterfile.inp"]
>>> puts $output $totalE
>>> In the output file, value of all the calculated energies are zero. This
>>> is the same if -bond or -elec is used as the energy type.
>>> Thank you.
>>> Best,
>>> Monika
>>> On Thu, Feb 1, 2018 at 10:06 PM, Onur Serçinoğlu <>
>>> wrote:
>>>> Hi Monika,
>>>> *couldn't execute "": no such file or directory*
>>>> I'm not 100% sure, but could it be that namdenergy can't locate the
>>>> namd2 executable? After all, the plugin utilizes namd2 exe to calculate the
>>>> energy of a given residue and you need to provide the path to the
>>>> executable if namd2 isn't in the executable search path of your system--001a113c862c7db7080564339555--

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