AMBER Archive (2008)

Subject: RE: AMBER: how to extract energy

From: WANG,YING (wangying_at_ufl.edu)
Date: Sun May 25 2008 - 08:57:20 CDT

Thanks a lot!!

If I use AMBER 9, could I decomposite the energy of individual
molecule?

Best,

Ying

On Fri May 23 23:07:41 EDT 2008, Ross Walker
<ross_at_rosswalker.co.uk> wrote:

> Hi Wang,
>
> Are you running this simulation in explicit solvent? If so then
> the PME
> routines etc are not strictly pairwise decomposable so you can't
> actually
> evaluate the energy of a single molecule. You can, however,
> obtain the
> internal energy for a molecule (bonds, angles, dihedrals etc). If
> you are
> running implicit solvent GB then you can do a pairwise
> decomposition to find
> an individual molecules contribution to the total energy.
>
> See idecomp on page 26 of the AMBER 10 manual.
>
> Good luck,
> Ross
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]
>> On Behalf
>> Of WANG,YING
>> Sent: Friday, May 23, 2008 6:08 PM
>> To: amber_at_scripps.edu
>> Subject: AMBER: how to extract energy
>>
>> Hi, Dear ambers,
>>
>> My system contain some molecules. The mdout give me the total
>> energy of the whole system. if I want to know the energy of one
>> of
>> the molecules but not the total energy of the whole system, how
>> can I do?
>>
>> If you know how to do could you tell me? Thanks a lot!!
>>
>>
>> Ying
>>
>>
>>
>>
>>
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>

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