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PBC setup in "Coor Analysis"
#37951 06/25/20 08:46 AM
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Hello.
When using PBC option by setting xbox ybox and zbox value in Coor Analysis command, does it mean it can only be used for NVT trajectory. If box dimensions not fluctuate too much in a NPT simulation, is it proper to use this option? And what box shape is available for this option? In coor hbond , only CUBIC , Truncated octahedron, and Rhombic dodecahedron are OK to use.

Last edited by Allen_123; 06/25/20 08:47 AM.
Re: PBC setup in "Coor Analysis"
Allen_123 #37954 06/25/20 11:30 AM
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For COOR ANALysis of NPT simulations the actual boxsize will be used for each step. Only orthorhombic PBC is supported, and you should setup your PBC (images or crystal commands) before the analysis using the same commands as were used for the production simulation.

Last edited by lennart; 06/25/20 12:48 PM.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: PBC setup in "Coor Analysis"
lennart #37955 06/25/20 12:49 PM
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Thank you for explaning

Last edited by Allen_123; 06/25/20 12:53 PM.
Re: PBC setup in "Coor Analysis"
Allen_123 #37961 07/07/20 12:46 PM
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Hello,

I changed the solana.src so that coor anal command could be used for hexagonal pbc box. Could anyone confirm correct or not? This corresponding to calculating distance between ref point and solvent atom when minimum image convention is met.


DDX=X(1,I) - REF(1)
DDY=X(2,I) - REF(2)
DDZ=X(3,I) - REF(3)
THETA=ONE2TY*PI/ONE8TY
IF(MINI) THEN
IF(ABS(DDX) > XBOX2 .AND. ABS(DDY) < YBOX2) THEN
DDX=DDX - SIGN(XBOX,DDX)
ENDIF
IF(ABS(DDX) > XBOX2 .AND. ABS(DDY) > YBOX2) THEN
XS=XBOX+COS(THETA)*XBOX
YS=YBOX*SIN(THETA)
DDX=DDX - SIGN(XS, DDX)
DDY=DDY - SIGN(YS, DDY)
ENDIF
IF(ABS(DDY) > YBOX2 .AND. ABS(DDX) < XBOX2) THEN
XS=COS(THETA)*XBOX
YS=YBOX*SIN(THETA)
DDX=DDX -SIGN(XS, DDX)
DDY=DDY -SIGN(YS, DDY)
ENDIF
IF(ABS(DDZ) > ZBOX2) DDZ=DDZ - SIGN(ZBOX,DDZ)
ENDIF

Re: PBC setup in "Coor Analysis"
Allen_123 #37962 07/07/20 01:01 PM
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I think for rdf determination, I'm able to get good results if I am only interested in H2O distribution very close to a reference site by applying reasonable mgn and rsph values and turning off pbc option.
In coor hbond command, however, there is no such distance I could vary, and therefore, I must use pbc option and I must change the code if I don't use the pbc box in the manual. Is that ture?

Last edited by Allen_123; 07/07/20 01:02 PM.
Re: PBC setup in "Coor Analysis"
Allen_123 #37965 07/08/20 06:38 PM
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Depends on what you want to do. One possible workaround is to process the trajectory with the MERGE RECEnter command and place the molecule of interest in the center of the box, and then use COOR HBOND on the recentered trajectory w/o PBC.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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