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#36934 - 04/06/18 11:45 AM Problem with EDIT MULT in Vibran
Maxime Louet Offline
Forum Member

Registered: 11/16/10
Posts: 1
Loc: France
Dear Charmm community,

I encounter a problem trying to multiply an eigenvector of a specific normal mode. I found in the documentation the command EDIT MULT MODE n SCALe real [atom-selection]. I used it but I didn't see any change in the vectors. Here is the exact script I'm running (on charmm Free Version 42b1 - gnu - linux):

<<<
* Used to modify a normal mode
* usage: $CHARMMEXEC < edit_nm.inp > edit_nm.log
*

DIMENS CHSIZE 3000000 MAXRES 3000000

! Read topology and parameter files
stream toppar_charmm.str

open read card unit 15 name build_nma.psf
read psf card unit 15
close unit 15

open read unit 10 card name nma_minimized.crd
read coor card unit 10
close unit 10

vibran nmod 200
open read file unit 40 name modes.mod
read norm file unit 40
print norm mode @modnu vect

edit mult mode 7 scale 5.81289219 sele ATOM * * * end

print norm mode @modnu vect

open write unit 52 name modes_@modnu.mod
write norm file unit 52
close unit 52

close unit 40
end

stop
>>>

Here's the output for vibran:

<<<
VIBRAN: Space allocated for 200 vectors of length 15567

VIBRAN> open read file unit 40 name modes.mod
VOPEN> Attempting to open::modes.mod::
OPNLGU> Unit 40 opened for READONLY access to modes.mod

VIBRAN> read norm file unit 40
TITLE> * GENERATED BY CHARMM-GUI ([url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG]HTTP://WWW.CHARMM-GUI.ORG[/url][/url][/url]) V2.0 ON NOV, 16. 2017. JOB
TITLE> * READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE
TITLE> * DATE: 3/20/18 18: 0:25 CREATED BY USER: maxime
TITLE> *

VIBRAN> print norm mode @modnu vect
Parameter: MODNU -> "7"

NORMAL MODES

7 4.16

VIBRATION MODE 7 FREQUENCY= 4.160949 TRANS ROT %= 0.000000
EIGENVALUE= 0.001468 ENERGY DERIVATIVE= 0.000000
TYPE 'FACT' 1.0000 MASS NORM STEP= 1.000000

EIGENVECTOR:
1 1 ASP N 0.01063 0.00849 -0.00857
2 1 ASP HT1 0.00970 0.00746 -0.00769
3 1 ASP HT2 0.01106 0.00866 -0.00897
4 1 ASP HT3 0.01162 0.00794 -0.00921
5 1 ASP CA 0.00994 0.01051 -0.00871
6 1 ASP HA 0.00881 0.01079 -0.00804
7 1 ASP CB 0.01114 0.01181 -0.00990
...
...
[many lines]
...
...

VIBRAN>

VIBRAN> edit mult mode 7 scale 5.81289219 sele ATOM * * * end
SELRPN> 5189 atoms have been selected out of 5189

VIBRAN>

VIBRAN> print norm mode @modnu vect
Parameter: MODNU -> "7"

NORMAL MODES

7 4.16

VIBRATION MODE 7 FREQUENCY= 4.160949 TRANS ROT %= 0.000000
EIGENVALUE= 0.001468 ENERGY DERIVATIVE= 0.000000
TYPE 'FACT' 1.0000 MASS NORM STEP= 1.000000

EIGENVECTOR:
1 1 ASP N 0.01063 0.00849 -0.00857
2 1 ASP HT1 0.00970 0.00746 -0.00769
3 1 ASP HT2 0.01106 0.00866 -0.00897
4 1 ASP HT3 0.01162 0.00794 -0.00921
5 1 ASP CA 0.00994 0.01051 -0.00871
6 1 ASP HA 0.00881 0.01079 -0.00804
7 1 ASP CB 0.01114 0.01181 -0.00990
...
...
[many lines]
...
...

VIBRAN>

VIBRAN> open write unit 52 name modes_@modnu.mod
Parameter: MODNU -> "7"

***** LEVEL 1 WARNING FROM *****
***** NO FORMATTING SPECIFICATION, IT WILL BE OPENED UNFORMATTED
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5

VOPEN> Attempting to open::modes_7.mod::
OPNLGU> Unit 52 opened for WRITE access to modes_7.mod

VIBRAN> write norm file unit 52
RDTITL> CLOSE UNIT 52
RDTITL> No title read.
VCLOSE: Closing unit 52 with status "KEEP"

VIBRAN> close unit 52
CLOLGU> ***** WARNING ***** Attempt to close unit that was not open.

VIBRAN>

VIBRAN> close unit 40
VCLOSE: Closing unit 40 with status "KEEP"

VIBRAN> end
>>>

As you read, there was no change in the vectors. The factor has not been applied. What am I doing wrong or missing/misunderstanding?

I tried many things including using the set of comparison coordinate and subsequently the EDIT INCL command with no luck. Any suggestion would be appreciated. Many thanks!

Maxime

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#36935 - 04/10/18 01:57 PM Re: Problem with EDIT MULT in Vibran [Re: Maxime Louet]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
PRINT NORM prints normalized vectors, since it is the direction that is of interest in most cases.
WRITE NORM CARD writes out the actual vector(s) to a text file.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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