AMBER Archive (2005)

Subject: Re: AMBER: Separating solvent and solute energy in the microcanonical mode

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Mar 17 2005 - 17:33:43 CST

here is one way to do it, there may be others:

use ptraj to strip out the water from the trajectory, then
use sander with imin=5 (check the manual, page 95) and read in
the trajectory file with maxcyc=1 and dx0=0.00000001.
you can then extract the energies form the output file.

another way to do it would be to use the MM-PBSA scripts.
you'd need to check the manual and examples for details.
there are also decomposition options in sander, again you'd need
to do some checking on it. look for "idecomp" in the manual.
I don't know if this would easily do what you want.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Mey Khalili wrote:

> Even so, can you tell me how to calculate each component separately?
>
> Thanks
> Mey
>
>
>
>>there is no reason that the total energy of the protein
>>should be conserved in the simulation. It is only the total
>>system energy that is constant- nothing is guaranteed
>>for components.
>>
>>===================================================================
>>Carlos L. Simmerling, Ph.D.
>>Associate Professor Phone: (631) 632-1336
>>Center for Structural Biology Fax: (631) 632-1555
>>Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
>>Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
>>===================================================================
>>
>>
>>
>>
>>Mey Khalili wrote:
>>
>>
>>
>>> Hi,
>>>
>>> I am trying to estimate the extent to which the total energy is
>>>conserved in microcanonical mode in AMBER. I ran Ala10 in a box of
>>>water in the NVE mode, without any coupling to the Berendsen bath as I
>>>know from the AMBER archive that this method does not keep the total
>>>energy as constant as the NVE mode.
>>> I ran the system for 90ps and then monitored the total, potential and
>>>kinetic energy of the entire system. The drift in the total energy is
>>>0.5% of the kinetic and 0.6% of the potential energy. But this is the
>>>TOTAL energy of the solvent plus the protein. How do I extract the
>>>protein's potential, kinetic and total energy to see to what extent the
>>>total energy of the protein is conserved?
>>>
>>> Thanks
>>>
>>> Mey
>>>
>>>
>>>
>>>-----------------------------------------------------------------------
>>>The AMBER Mail Reflector
>>>To post, send mail to amber_at_scripps.edu
>>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>>
>>>
>>>
>>>
>>-----------------------------------------------------------------------
>>The AMBER Mail Reflector
>>To post, send mail to amber_at_scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>>
>
>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu