From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 09 2010 - 07:04:49 CDT
Hi Lada,
I should have looked at your selections more closely before replying...
if you only specify a single selection, namdenergy will return *all*
interactions involving those atoms (so, in your case, for example, you
get all the bonds that each of your CB atoms has with anything else). If
you want only the interaction *between* those two atoms, you need to
specify them as two separate selections. Let me know if this does not
resolve your question.
Best,
Peter
On 09/09/2010 04:51 AM, Lada Biedermannová wrote:
> Hi Peter,
>
> Attached please find the namd-temp.namd config file and the
> namd-temp.pdb for my small testing system of ALA-SER dipeptide.
>
> Thanks,
> Lada
>
>
> On 9 September 2010 02:19, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
>> Hi Lada,
>> Could you send the config file generated by namdenergy (namd-temp.namd)
>> and the top 10 lines or so of your pdb?
>> Thanks,
>> Peter
>>
>> On 09/08/2010 05:16 AM, Lada Biedermannová wrote:
>>
>>> Hi all,
>>>
>>> I am using the NAMD Energy plugin to get internal energies of a
>>> selection of my system. However, I am confused by the fact that I am
>>> getting a non-zero Bond, Angle and Dihed energies even for a selection
>>> of two atoms that are not bonded, eg. for two CB atoms as shown below.
>>> Could somebody explain where these numbers come from?
>>>
>>> Thanks,
>>>
>>> Lada Biedermannova
>>>
>>> ------------------------
>>> namdEnergy) Computing energy for selection:
>>> namdEnergy) index 6 16
>>>
>>> namdEnergy) Running:
>>> namdEnergy) /sw/mcm/app/namd/NAMD_2.6_Linux-i686/namd2 namd-temp.namd
>>>
>>> Frame Time Bond Angle Dihed
>>> Impr Elec VdW Conf Nonbond
>>> Total
>>> 0 0 +0.1559 +0.0737 +1.1857
>>> +0 -0.9343 -0.0181 +1.4153 -0.9524
>>> +0.4629
>>>
>>>
>>
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