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image issues in minization and energy calculation
#35618 04/09/16 05:14 AM
Joined: Mar 2007
Posts: 148
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jeffrey Offline OP
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Joined: Mar 2007
Posts: 148
Hi All,

I am doing a crystal minimization and find very different results with "image byres sele resn lig end" and "image byres xcen ?xave ycen ?yave zcen ?zave sele resn lig end".

Here is the related input:
----------------------------
coor stat select all end
Crystal Define @shape @a @b @c @alpha @beta @gamma
Crystal Build cutoff 14.0 noperations 7
(x+1/2,-y+1/2,-z+1/4)
(-x+1/2,y+1/2,-z+3/4)
(-x,-y,z+1/2)
(-y,-x,-z+1/2)
(-y+1/2,x+1/2,z+3/4)
(y+1/2,-x+1/2,z+1/4)
(y,x,-z)

!image byres xcen ?xave ycen ?yave zcen ?zave sele resn LIG end
image byres sele resn LIG end

Update inbfrq -1 imgfrq -1 ihbfrq 0 -
ewald pmewald lrc fftx 8 ffty 8 fftz 40 -
kappa 0.34 order 6 CTOFNB 12.0 CUTNB 14.0 QCOR 1.0 -
fshift atom vatom vfswitch

mini sd lattice nstep 100
mini abnr lattice nstep 2000 tolenr 1.e-5
----------------------------------------------------

-------1st energy with "image byres xcen ?xave ycen ?yave zcen ?zave sele resn lig end":
MINI MIN: Cycle ENERgy Delta-E GRMS Step-size
MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
MINI EXTERN: VDWaals ELEC HBONds ASP USER
MINI IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
MINI EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
MINI LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
MINI> 0 -23.29294 0.00000 17.24350 0.02000
MINI INTERN> 8.90852 20.80160 0.00000 36.77309 0.02627
MINI EXTERN> 6.51841 -12.64885 0.00000 0.00000 0.00000
MINI IMAGES> -21.18639 -6.68863 0.00000 0.00000 0.00000
MINI EWALD> 0.78541 -234.64109 178.57127 0.00000 0.00000
MINI LRCor> -0.51257 -1.02499
----------------------


-------1st energy with "image sele resn lig end":
MINI MIN: Cycle ENERgy Delta-E GRMS Step-size
MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
MINI EXTERN: VDWaals ELEC HBONds ASP USER
MINI IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
MINI EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
MINI LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
MINI> 0 -6.17001 0.00000 17.25917 0.02000
MINI INTERN> 8.90852 20.80160 0.00000 36.77309 0.02627
MINI EXTERN> 6.51841 -12.64885 0.00000 0.00000 0.00000
MINI IMAGES> -8.73618 -2.01591 0.00000 0.00000 0.00000
MINI EWALD> 0.78541 -234.64109 178.57127 0.00000 0.00000
MINI LRCor> -0.51257 -1.02499
-------------

I don't know how CHARMM treats the image differently with different center settings. I appreciate any explanation about this.

Best,

Jeffrey

Re: image issues in minization and energy calculation
jeffrey #35619 04/09/16 03:11 PM
Joined: Sep 2003
Posts: 8,447
rmv Online Content
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Joined: Sep 2003
Posts: 8,447
The CRYSTAL commands in CHARMM use standard crystallography conventions.

Crystallographic transformations are defined in the context of specific centers and axes, and the molecules MUST be placed with respect to these. The center can be the origin or it can be some other location, but it is usually NOT the geometric center of the atoms. With transformations other than translation, using a different center is expected to give different results, and can cause problems.


Rick Venable
computational chemist


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