From: Lada Biedermannová (lada.biedermannova_at_img.cas.cz)
Date: Thu Sep 09 2010 - 03:51:12 CDT
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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