Re: NAMD Energy types

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 09 2010 - 20:40:15 CDT

Hi Lada,
If you want to get *specific* bonds, you should use the measure energy
command (see
http://www.ks.uiuc.edu/Research/vmd/current/ug/node133.html). If you
want all bonds that a group of atoms are involved in (which is in my
experience a more common usage case), that's where namdenergy comes in.
Best,
Peter

On 09/09/2010 09:16 AM, Lada Biedermannová wrote:
> Hi Peter,
>
> Thanks for the clarification.
>
> The thing is that if I specify the two atoms as two separate
> selections, I only get the interaction energies, whereas I would like
> to also get the internal energies (Bond energy for pairs of atoms,
> etc). Is there any way to work around this?
>
> Best,
> Lada
>
>
>
> On 9 September 2010 14:04, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
>> 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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