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Help with Script to calculate trajectory rms matrix
#6655 05/14/05 06:10 PM
Joined: Mar 2005
Posts: 42
L
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L
Joined: Mar 2005
Posts: 42
hello

I would like to create a rms matrix for my trajectory (a matrix where entry aij is the rms beetween the i-th and j-th trajectory frame) I Thought it would be done using a loop over traj read (dynamc.doc) defining each coordinate frame as the comparison cordinate, and then using correl rms to obtain the rms time series related to the traj read strucure, and then combining the outputs into a matrix. To do it, I used a mixture from lennart's rms-rgyr.inp and other scripts:

*FILENAME: Rmsd-Matrix.inp
*PURPOSE: compute
*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003

read rtf card name $CHM_PGI_HOME/toppar/top_all22_prot.inp
read para card name $CHM_PGI_HOME/toppar/par_all22_prot.inp
read psf card name "1YPC-din35.psf"

open unit 51 read unform name din35-merged.dcd

!OPENING TRAJECTORY TO BE READED WITH TRAJ READ
trajectory firstu 51 nunit 1 skip 1000 begin 1000 stop 125000
set counter 1
label loop
!DEFINING THAT EACH FRAME IS GOING TO BE CONSIDERED THE COMPARISON COORDINATE
trajectory read comp
open unit 11 write form name frame@counter.dat
write title unit 11
* time rmsd
*
correl maxtime 10000
enter v1 rms
traj firstu 51 nunit 1 begin 1000 skip 1000 stop 125000
write v1 dumb time unit 11
*hi
*
end
incr counter by 1
if counter lt 126 goto loop
stop

the code works well in the first iteration, but when it read "trajectory read comp" for the second time it exits without FORTRAN STOP or any complain. I thougt the problem would be in using a same trajectory in two loops, so I try to read the .dcd file twice using another open statement into a second unit (i.e, unit 52), but the program exits with FORTRAN STOP. I dont know how this can be fixed. Can someone give me a hand???

Gracias, gracias

leonardo

Last edited by Leonardo; 05/14/05 06:12 PM.

Leonardo Sepulveda Durán Universidad de Chile
Re: Help with Script to calculate trajectory rms matrix
Leonardo #6656 05/14/05 06:50 PM
Joined: Sep 2003
Posts: 8,485
rmv Offline
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Try using a different unit number for the TRAJ READ setup; the job quits because you've used the same unit number both for that and within CORREL.


Rick Venable
computational chemist

Re: Help with Script to calculate trajectory rms matrix
Leonardo #6657 05/14/05 07:44 PM
Joined: Sep 2003
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try the RMSDyn command instead, it does exactly this.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Help with Script to calculate trajectory rms matrix
lennart #6658 05/14/05 08:01 PM
Joined: Sep 2003
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rmv Offline
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The RMSDyn command is described in dynamc.doc


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