Re: NAMD Energy types

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Sep 17 2010 - 14:39:29 CDT

Hi,

It looks like Lada has found an old bug from 2002. The self-interaction
code includes bond/angle/dihedral/improper energy only if the *first* atom
in the bond/... is selected. That's not remotely the right thing to do.

-Jim

On Thu, 9 Sep 2010, Peter Freddolino 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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