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Joined: Jan 2006
Posts: 70
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mittko Offline OP
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Joined: Jan 2006
Posts: 70
On of the examples in the COOR ANAL for calculating g(r) is:

! g(r) for GLY3 NH - the water oxygens - with excluded volume correction
open unit 21 read unform name @9pept500.cor
open unit 31 write form name @9pept500.gn3ox1
coor anal select type OH2 end -
site multi select atom pept 3 H end -
EXVC select segid pept end -
MCPoints 2000 MCSHells 20 RPRObe 1.7 -
firstu 21 nunit 1 skip 50 - ! trajectory specification
isdist 31 - ! flag to do the solvent-solvent g(r)
mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR
rsph 999.9 - ! we use ALL waters for the calculation
xbox @6 ybox @7 zbox @8 ! and we did use PBC

I do not understand whether or not other types of PBC are supported (like OCTA, RHDO). This seems to support only rectangular boxes. If I MERGE RECEnter my solute, do I need to specify PBC conditions if I am primarily interested in g(r) in the vicinity of my solute? If I do, what would these be if I am using an OCTA unit cell?

Thanks.

Joined: Sep 2003
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True, only a simple orthorhombic box is supported, but MERGE RECEnter is a general way to handle the common case that you have.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  BRBrooks, lennart, rmv 

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