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#370 - 11/21/06 08:06 PM Re: rmsd-rgyr.inp [Re: r_hz]
prakash Offline
Forum Member

Registered: 10/04/05
Posts: 206
from the example
open unit 51 read unform name traj1.cor
open unit 52 read unform name traj2.cor
correl maxtime 10000
enter v1 rms
enter v2 gyra

traj firstu 51 nunit 2 begin 10500 skip 500 end 55000

why there is two *.cor files , both these files have same values repeated twice or values of nsavc starting from 10500 to 55000 partly filled in each other.

#371 - 11/21/06 08:49 PM Re: rmsd-rgyr.inp [Re: prakash]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8290
Loc: 39 03 48 N, 77 06 54 W
The latter is the usual case; perhaps steps 500 thru 30000 are in the first file, and steps 30500 thru 60000 are in the second, so both are needed to analyze 10500 thru 55000.
Rick Venable
computational chemist

#372 - 11/21/06 09:14 PM Re: rmsd-rgyr.inp [Re: rmv]
prakash Offline
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Registered: 10/04/05
Posts: 206
thank you

#32003 - 05/29/13 02:27 PM Re: rmsd-rgyr.inp [Re: lennart]
swmmr1928 Offline
Forum Member

Registered: 10/07/12
Posts: 24
I ran the script using psf, pdb, and traj made from your merge script and deleted water.
The error I get running the rmsd-rgyr script is:
At line 959 of file dynio.f
Fortran runtime error: End of file

The output file is attached.
This is the input file:
!*FILENAME: rmsd-rgyr.inp
!*PURPOSE: compute rmsd vs initial structure and radius of gyration from
!*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
!unix environment variable CHM_HOME points to CHARMM installation
stream toppar.str

read psf card name "new_psf.psf"
open unit 2 card read name -
read coor pdb resid unit 2

! put reference coordinates into comparison set as well
coor copy comp
open unit 11 write form name rmsd.dat
write title unit 11
* time rmsd
open unit 12 write form name rgyr.dat
write title unit 12
        * time rgyr
! assume this is a trajectory where overall translation/rotation has been
!removed and
! without water or other unnecessary things

open unit 51 read unform name -

correl maxtime 10000000
enter v1 rms
enter v2 gyra

traj firstu 51

write v1 dumb time unit 11

write v2 dumb time unit 12


test.out.txt (433 downloads)

#35170 - 08/04/15 07:38 PM Re: rmsd-rgyr.inp [Re: lennart]
milii_miller Offline
Forum Member

Registered: 07/22/15
Posts: 9
im doing this for a .pdb but show me this

The following time series will be filled:

VOPEN> Attempting to open::1_wt.pdb::

***** LEVEL -2 WARNING FROM *****
***** Apparent problem with endianness

#35171 - 08/05/15 02:41 AM Re: rmsd-rgyr.inp [Re: lennart]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4700
Loc: ~ 59N, 15E
This script analyzes the time-dependent evolution of RMSD and RGYR from a trajectory. To analyze a single coordinate set contained in a PDB file:

read coor pdb name 1_wt.pdb
read coor pdb name ref.pdb comp
coor rgyr
coor orient
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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