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Question about "image byresi"
#35480 12/31/15 05:45 AM
Joined: Mar 2007
Posts: 148
J
jeffrey Offline OP
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J
Joined: Mar 2007
Posts: 148
Dear CHARMM users,

In my parameter set of the minimization,I noticed that the use of the following two IMAGE sets gives different energies:
IMAGE BYRESI sele resname @resn end

OR

coor stat sele resname @resn end
IMAGE BYRESI xcen ?xaver ycen ?yaver zcen ?zaver sele resname @resn end

My system only contains one molecule for crystal simulations.
With "IMAGE BYRESI sele resname @resn end", the energy is:
----------------------
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER EXTERN: VDWaals ELEC HBONds ASP USER
ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
ENER EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
ENER LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
ENER> 0 -188.27453 0.00000 8.30574
ENER INTERN> 1.44056 4.63331 0.00000 12.08342 0.25982
ENER EXTERN> 2.45864 -38.76706 0.00000 0.00000 0.00000
ENER IMAGES> 1.83117 -6.50679 0.00000 0.00000 0.00000
ENER EWALD> 4.31444 -270.84924 101.08009 0.00000 0.00000
ENER LRCor> -0.25290 -0.50573
---------- --------- --------- --------- --------- ---------
----------------------

With "IMAGE BYRESI xcen ?xaver ycen ?yaver zcen ?zaver sele resname @resn end", the energy is:
----------------------
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER EXTERN: VDWaals ELEC HBONds ASP USER
ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
ENER EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
ENER LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
ENER> 0 -120.92121 0.00000 64.60565
ENER INTERN> 1.44056 4.63331 0.00000 12.08342 0.25982
ENER EXTERN> 2.45864 -38.76706 0.00000 0.00000 0.00000
ENER IMAGES> 62.49159 0.18611 0.00000 0.00000 0.00000
ENER EWALD> 4.31444 -270.84924 101.08009 0.00000 0.00000
ENER LRCor> -0.25290 -0.50573
---------- --------- --------- --------- --------- ---------
----------------------

The result shows different energy values for IMNBvdw and IMELec.

My question is how the different center of image produces different energies? Will this affect the minimized conformation?

I read the following description from the manual but still cannot get a clear understanding and thus request your help.

---------------description of "IMAGE byresi" in CHARMM manual:
"
During dynamics, a particular water may become far from
the rest of the primary structure. The centering features allows one of its
image (the one closest to the primary space) to become the primary water.

It is also useful when setting up a crystal calulation. With a single
update, the "best" image choice of all solvent molecules may be made.
One example of this is the netropsin crystal where one of the published
sulfate groups is quite far from the primary netropsin. This command is
required for a pure solvent simulation where solvent can freely diffuse.

The execution of this command only sets up data used during the image
update. There is only one value each for XCEN, YCEN, and ZCEN. If these
values are not specified in any IMAGE command, then they are not modified
(default 0.0).
"

Thanks a lot!

Jeffrey

Re: Question about "image byresi"
jeffrey #35481 12/31/15 08:13 PM
Joined: Sep 2003
Posts: 8,498
rmv Online Content
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Online Content
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Joined: Sep 2003
Posts: 8,498
First, this is the wrong forum; the question has nothing to do with the force field parameters.

Besides that, there are simply too many missing details. Is this an attempt to simulate a crystal structure of a single small molecule?

Try a more complete post in an appropriate forum; see READ BEFORE POSTING for guidance on choosing a forum and other tips for posting.


Rick Venable
computational chemist


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