Re: NAMD Energy types

From: Lada BiedermannovŠ (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 BiedermannovŠ 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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