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Baloo Offline OP
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Hello,

I am trying to find the rmsf of all the frames of the trajectory wrt every frame, so its kind of iteration that goes on.

-Is there any way I can pick the desired frame of trajectory at once and not reading all the previously occuring frames? I can then put it in comparison set.

What I am doing now is just incrementing the counter to set the value of begin for "traj iread 20 nread 1 begin @counter skip ?skip stop ?nstep", so that trajectory reading could start exactly at that frame and then put in comparison set. For this I need to open and read the trajectory file. Since I have to see the rmsf of all the frames of trajectory wrt this particular frame (comparison set), I need to read this trajectory again with the default begin value (first frame of the trajectory) "traj iread 20 nread 1 begin ?start skip ?skip stop ?nstep" and this gives me the following error

***** LEVEL 0 WARNING FROM <TRAJIO> *****
***** INITIATING NEW TRAJECTORY I/O WHILE STILL READING OLD ONE
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

I would appreciate if someone can give me clues or refer me to threads where this kind of issue has been touched, as I have searched it on forum but donot find any.

Best Wishes,
Baloo

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I assume that you are interested in the RMS Deviation (not Fluctuation) between frames. Try the RMSDyn command (dynamc.doc).


Lennart Nilsson
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Baloo Offline OP
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Yes, you are right, I am sorry it is RMSD, let me try RMSDyn command.

-Baloo

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Baloo Offline OP
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Hi,

It seems to me that RMSDyn is not supported. As when I try to intialize this command like

RMSDYN firstu 20 secu 21 ORIEnt RMS iwrite 41

charmm gives me an error...


CHARMM> RMSDYN firstu 20 secu 21 ORIEnt RMS iwrite 41

***** LEVEL -1 WARNING FROM <RMSDYN> *****
***** UNSUPPORTED OPTION
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

Best
-Baloo

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rmv Online Content
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From dynamc.doc--

NB! BEGIN, SKIP and STOP have to be specified to allow proper
memory allocation! The TRAJ QUERY command can retrieve these values
The trajectory(ies) are read into memory before calculations begin;
Memory usage may be reduced by decreasing the number of selected atoms,
and by reducing the number coordinate sets (frames) used - increase SKIP

The error message, which is from RMSDyn, is simply not very informative, a lot like the documentation for this command. However, the above implies you must include BEGIN, SKIP and STOP as part of the command.

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Baloo Offline OP
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This time I put all the necessary files open prior to intiate the RMSDyn command. My input looks like this..

---------
! open trajectory to read
open unit 20 read file name dyna.dcd
traj query unit 20


!since same trajectory is used. I want to pick every frame of the same trajectory and to find the RMSD of all the frames of this same trajectory wrt picked frame.
set frame 0
label loop

! open the file to write the matrix
open unit 44 write form name "rmsd-matrix-wrt-frame@frame.dat"

RMSDyn firstu 20 nunit 1 begin @frame skip ?skip stop @frame secu 20 nun2 1 beg2 ?start skp2 ?skip stp2 ?nstep ORIEnt RMS iwrite 44 matrix

incr frame by 1
if frame lt ?nstep goto loop

---------

I still get the following error..

CHARMM> RMSDyn firstu 20 nunit 1 begin @frame skip ?skip stop @frame -
CHARMM> secu 20 nun2 1 beg2 ?start skp2 ?skip stp2 ?nstep ORIEnt RMS iwrite 44 matrix
Parameter: FRAME -> "0"
Parameter: FRAME -> "0"
RDCMND substituted energy or value "?SKIP" to "1"
RDCMND substituted energy or value "?START" to "0"
RDCMND substituted energy or value "?SKIP" to "1"
RDCMND substituted energy or value "?NSTEP" to "1716"

***** LEVEL -1 WARNING FROM <RMSDYN> *****
***** UNSUPPORTED OPTION
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5


Best
-Baloo

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rmv Online Content
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It could be a bug; which CHARMM release version(s) exhibit this behavior?

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Baloo Offline OP
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I tried with charmm27, 28, 30, 32, 33, 34

Every time I get the same error. Is there any solution or clues to my problem.

Best
-Baloo

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rmv Online Content
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The source code seems to imply that ORIENT must be the 2nd word on the command line; the bad documentation tends to obscure this fact.

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Baloo Offline OP
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It seems to work if I put ORIENT at the second position. However, I now encounter another problem.

My source code is like..

----------
! open trajectory to read
open unit 20 read file name dyna.dcd
traj query unit 20

! open the file to write the matrix
open unit 44 write form name "rmsd-matrix.dat"

RMSDyn orient rms firstu 20 nunit 1 begin ?start skip ?skip stop ?nstep secu 20 nun2 1 beg2 ?start skp2 ?skip stp2 ?nstep iwrite 44 matrix

----------
The error is...

CHARMM> RMSDyn orient rms firstu 20 nunit 1 begin ?start skip ?skip stop ?nstep -
CHARMM> secu 20 nun2 1 beg2 ?start skp2 ?skip stp2 ?nstep iwrite 44 matrix
RDCMND substituted energy or value "?START" to "0"
RDCMND substituted energy or value "?SKIP" to "1"
RDCMND substituted energy or value "?NSTEP" to "1716"
RDCMND substituted energy or value "?START" to "0"
RDCMND substituted energy or value "?SKIP" to "1"
RDCMND substituted energy or value "?NSTEP" to "1716"
TRAJ: INITIATING READ OF TRAJECTORIES, OPTIONS;
FIRSTU = 20 SECNDU = 20 BEGIN = 0 SKIP= 1 STOP = 1716

READING TRAJECTORY FROM UNIT 20
NUMBER OF COORDINATE SETS IN FILE: 1716
NUMBER OF PREVIOUS DYNAMICS STEPS: 0
FREQUENCY FOR SAVING COORDINATES: 1
NUMBER OF STEPS FOR CREATION RUN: 1716

TITLE> Created by DCD plugin
TITLE> REMARKS Created 19 July, 2008 at 21:32
TITLE> *
***** WARNING ***** BEGIN= 0 Was not specified. It has been set to: 0
***** WARNING ***** ONLY 1715 OF THE 1716 REQUESTED STEPS WERE IN THE INPUT FILE(S)

1716 CORD RECORDS READ FROM 1 UNITS STARTING WITH UNIT 20
RUNNING FROM STEP 0 TO 1715 SKIPPING 1 STEPS BETWEEN RECORDS
Time step was 1.000000 AKMA time units.
ERROR in READCV -- Bad ISTATS, -1 passed.
*** LEVEL -3 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.


Best
-Baloo

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