Note that in general these kinds of decomposition are difficult. Unless the potential is pairwise decomposable (and neither PME or GB are), these energies are not well-defined. The most useful variants involve running multiple (2 or 3) separate calculations on subsets of the system to do it. You can always use "strip" to generate subsets before using the energy routines to get the energy of the remaining atoms.
HTH,
Jason
> On Mar 10, 2016, at 11:37 AM, Song-Ho Chong <chong.sookmyung.ac.kr> wrote:
>
> I see ... thanks ... and looking forward to seeing further progress.
>
> Song-Ho
>
> 2016-03-11 1:07 GMT+09:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> On Thu, Mar 10, 2016 at 8:51 AM, Song-Ho Chong <chong.sookmyung.ac.kr>
>> wrote:
>>>
>>> I just wonder whether 'eander' accepts one or two masks.
>>> The whole purpose that I wrote new codes is to compute energy
>>> for specific regions and for interaction between two specific regions
>>> of interest (since if only the total energy was what I want I could
>>> use sander API).
>>
>> Actually it currently uses no masks - the sander API has not
>> progressed to the point where energy decomposition is easy to do. It's
>> on the to-do list. Right now the 'esander' action basically serves the
>> same function as 'imin=5' in sander, but with cpptraj's trajectory
>> format parsers and parallelism.
>>
>> -Dan
>>
>>>
>>> Song-Ho
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 10 2016 - 10:00:03 PST
