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getting wrong rmsd
#37049 07/17/18 02:02 PM
Joined: Oct 2017
Posts: 42
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Rohit Offline OP
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it is giving me wrong RMSD values. I dont understand why.
when i comment outer loop it give correct values.

Code:
!================================================================
! read topology and parameters, and structure
!================================================================

READ PSF CARD NAME "./../eqf10/pu8_heq.psf"
READ COOR PDB NAME "./../eqf10/pu8_heq.pdb"

set i = 0
label loopbegin

coor copy comp
define backbone select segid PRT .AND. (type CA .or. type C .or. type N .or. type O) end
open unit 22 write form name ./../anal/recen/@i/rmsd_j0.@i.dat
open unit 51 read file name ./../anal/recen/@i/unfold_1le0.job0.@i.recen.dcd
traj iread 51 nskip 1 begin 0 stop 10000000
calc time = 1.0

label loopinner
traj read
coor orient rms select backbone end
write title unit 22
* @time ?rms
*
incr time by 1.0
if @time .le. 4000 then goto loopinner

incr i by 1
if @i .le. 48 then goto loopbegin
stop

Re: getting wrong rmsd
Rohit #37063 07/20/18 09:35 AM
Joined: Sep 2003
Posts: 394
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You need to move the line "coor copy comp"
to be outside of the outer loop.

With the way it's written, you're resetting the reference coordinates to the last frame of the previous file.

Re: getting wrong rmsd
Rohit #37066 07/20/18 10:47 AM
Joined: Oct 2017
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Rohit Offline OP
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oh i didn't see that.

thank-you for the help.


Moderated by  BRBrooks, lennart, rmv 

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