Re: Calculate energy of a residue using NAMD energy

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Feb 01 2018 - 21:59:53 CST

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 <monikamadhavi_at_gmail.com>
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 <onursercin_at_gmail.com>
> 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.
>>
>> When calling namdenergy, try this:
>>
>> namdenergy -all -sel $sel -par myparameterfile.inp -exe pathtothenamd2exe
>>
>> Replace pathtothenamd2exe with the full path of namd2 exe in the remove
>> server.
>>
>> Best,
>> Onur
>>
>> 2018-02-01 2:25 GMT+03:00 Monika Madhavi <monikamadhavi_at_gmail.com>:
>>
>>> Hi Peter,
>>>
>>> I am using VMD installed on the cluster so I have no idea whether they
>>> have installed the latest version. I used the syntax given in the link you
>>> sent but, that's the error I get. May be I should first try the script with
>>> VMD on my personal computer so that I can track the error.
>>>
>>> Thanks anyway.
>>> Best,
>>> Monika
>>>
>>> On Wed, Jan 31, 2018 at 12:51 PM, Peter Freddolino <petefred_at_umich.edu>
>>> wrote:
>>>
>>>> Dear Monika,
>>>> namdenergy is a proper vmd plugin. Is there any reason that you're
>>>> trying to use an old downloaded version rather than using the package that
>>>> comes with vmd?
>>>> package require namdenergy
>>>> should make the text interface available. See
>>>> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/ for how to use
>>>> it.
>>>> Best,
>>>> Peter
>>>>
>>>> On Mon, Jan 29, 2018 at 10:22 PM, Monika Madhavi <
>>>> monikamadhavi_at_gmail.com> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> I want to calculate the total energy of a specific residue (a water
>>>>> molecule) at each frame. It is suggested that this can be done using NAMD
>>>>> energy plugin. However, I would like to do the job through a script because
>>>>> my trajectory is in a remote server.
>>>>>
>>>>> I tried the following.
>>>>> obtained the code in this link and created a .tcl file called
>>>>> namdenergy.tcl in the folder where I have my script.
>>>>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-7
>>>>> 277/namdenergy.tcl
>>>>>
>>>>> Then I wrote a different tcl script with
>>>>> source namdenergy.tcl
>>>>> namd energy -all -sel $sel -par myparameterfile.inp
>>>>>
>>>>> Here I specified the parameter file because my parameter file is
>>>>> different from the common charmm parameter file. However, I am getting the
>>>>> following error
>>>>>
>>>>> invalid command name "::FinderTool::find"
>>>>>
>>>>> I would be grateful for a guidence to correctly use the namd energy to
>>>>> calculate energies of some selected atomselections.
>>>>>
>>>>> Thank you.
>>>>> Best,
>>>>> Monika
>>>>>
>>>>> --
>>>>> W.A.Monika Madhavi
>>>>> Lecturer (Probation),
>>>>> Department of Physics,
>>>>> University of Colombo.
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> W.A.Monika Madhavi
>>> Lecturer (Probation),
>>> Department of Physics,
>>> University of Colombo.
>>>
>>
>>
>
>
> --
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
>

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