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 #2364 - 08/02/04 10:14 AM non rectangular box beginner Forum Member Registered: 07/19/04 Posts: 165 Hi All,Please suggest me the input script to build a water box angles of 90 90 and 60 degrees!!!!Thx in advance. Top
 #2365 - 08/02/04 01:40 PM Re: non rectangular box BRBrooks Forum Member Registered: 09/02/03 Posts: 394 Loc: Rockville, Maryland Please look at crystl.doc You want the "HEXA" (hexagonal) unit cell if you want the angles to be fixed. Top
 #2366 - 08/03/04 04:55 AM Re: non rectangular box beginner Forum Member Registered: 07/19/04 Posts: 165 Dear Professor Brooks,Thank you very much for your response and suggestion.I have just started to learn charmm. I feel very confused on charm command up to now.I want to construct a water box with a = b # c in length and a = b = 90 degree and c = 60 degree in angle. After that my structure will be immersed in a water box and will be simulated on periodic boundary condition using images file.Following is my input file; it is assumed that RTF and PARAM files have been opened and readREAD COOR CARD FREE* The coordinates for the water molecule*31 1 TIP OH2 .00000 .06577 .00000 2 1 TIP H1 .75902 -.52198 .00000 3 1 TIP H2 -.75907 -.52195 .00000 set 1 1set 2 3.27926label linegene so@1 duplicate solvcoor duplicate sele segid solv end sele segid so@1 endcoor trans xdir @2 sele segid so@1 endincr 1 by 1incr 2 by 3.27926if 1 le 14 goto lineset 1 1label 2linejoin solv so@1 renumberincr 1 by 1if 1 le 14 goto 2lineopen write unit 12 card name "water_line.pdb"write coor pdb unit 12close unit 12set 1 1set 2 1.8933label planegene so@1 duplicate solvcoor duplicate sele segid solv end sele segid so@1 endcoor trans ydir @2 sele segid so@1 endincr 1 by 1incr 2 by 3.104if 1 le 9 goto planeset 1 1label 2planejoin solv so@1 renumberincr 1 by 1if 1 le 9 goto 2planeopen write unit 12 card name "water_plane.pdb"write coor pdb unit 12close unit 12set 1 1set 2 3.104label boxgene so@1 duplicate solvcoor duplicate sele segid solv end sele segid so@1 endcoor trans zdir @2 sele segid so@1 endincr 1 by 1incr 2 by 3.104if 1 le 9 goto boxset 1 1label 2boxjoin solv so@1 renumberincr 1 by 1if 1 le 9 goto 2box!coor orientopen write unit 12 card name "water_box.pdb"write coor pdb unit 12close unit 12coor statstop;( I have no idea how to set the angel to solve my problem.Any way, to construct a water box by using crystal option in charm, it is not necessary to define the position (coordinate) of the water (ie read…water.crd on the1st step), is it?Thank you in advance. Top
 #2367 - 08/09/04 10:01 AM Re: non rectangular box lennart Forum Member Registered: 09/25/03 Posts: 4761 Loc: ~ 59N, 15E There is no need to construct all the atom positions for all individual water molecules, you can start with a box of water and adapt it to your needs. See eg solvent-box.str in the Script Archive forum. To obtain coordinates for a non-orthorombic unit cell you can start from an orthorombic system (or any other geometry if you like), which is large enough to completely enclose the system you want to end up with. Then define your crystal and delete atoms outside the final primary box, like this: ```code: crystal define .... crystal build cutoff 14.0 image byres sele segid wat end coor copy comp update cutim 14.0 ! ! find and delete atoms that have changed position - ! they are outside the primary box coor diff comp scalar xcomp ipow 2 scalar xcomp store 1 scalar ycomp ipow 2 scalar ycomp +store 1 scalar zcomp ipow 2 scalar zcomp +store 1 scalar wcomp recall 1 delete atom sele .byres. prop wcomp .gt. 0.0 end ``` _________________________ Lennart NilssonKarolinska InstitutetStockholm, Sweden Top
 #2368 - 08/17/04 04:52 AM Re: non rectangular box beginner Forum Member Registered: 07/19/04 Posts: 165 Dear Professor Lennart Nilsson,Thanks you very much for your suggestion.Yours sincerely, Top

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