Re: Fwd: Cannot find colvar dih1 (dih colvars)

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Dec 23 2014 - 15:35:37 CST

Hi Francesco,

My guess is that there is a syntax error in the file — a missing "}"
or something of the sort. The general way to troubleshoot this is to
try to localize the problem. Start with something simple and add more
and see when the problem arises. Can you get it to work with just one
dihedral? Or just two? Can you whittle down the complexity (for
example, by commenting out lines) of the current file until it works?
This might help you to find the problem. Another option is to write a
script to generate the config file in which you can put safeguards to
ensure that you don't have missing braces, etc.

Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Tue, Dec 23, 2014 at 3:01 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> With the .in file containing colvars dih1 and dih2 only, the latter is read
> correctly. However, dih1 was not found
>
> Collective variables initialized, 1 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new "harmonic" instance.
> colvars: # name = MOL_dihe_harmonic
> colvars: # colvars = { dih1, dih2 }
> colvars: Error: cannot find a colvar named "dih1".
> colvars: If this error message is unclear, try recompiling with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> I can not understand what is wrong about the first colvars named "dih1".
> Aside from this, where 24 colvars too many?
>
> thanks for advice
>
> francesco pietra
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Tue, Dec 23, 2014 at 9:23 PM
> Subject: Fwd: Cannot find colvar dih1 (dih colvars)
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> I forgot to add that from colvars code I had noticed
>
> }
> 00208
> 00209 if (!colvars.size()) {
> 00210 cvm::log ("Warning: no collective variables defined.\n");
> 00211 }
>
> however could not relate "size" with my colvars.
>
> farncesco pietra
>
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Tue, Dec 23, 2014 at 6:15 PM
> Subject: Cannot find colvar dih1 (dih colvars)
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> Hello:
> New to dih colvars (Linux-multicore-64 namd2.10, minimization), I was unable
> to have colvars read:
>
> log file:
> colvars: Reading new configuration from file "./MOL_dihe_colvars.in":
> colvars: # indexFile = "" [default]
> colvars: # analysis = off [default]
> colvars: # colvarsTrajFrequency = 100 [default]
> colvars: # colvarsRestartFrequency = 100 [default]
> colvars: # colvarsTrajAppend = off [default]
> colvars: Warning: no collective variables defined.
> colvars: Collective variables initialized, 0 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new "harmonic" instance.
> colvars: # name = MOL_dihe_harmonic
> colvars: # colvars = { dih1, dih2, dih3, dih4, dih5, dih6, dih6, dih7,
> dih8, dih9, dih10, dih11, dih12, colvars, dih13, dih14, dih15, dih16, dih17,
> dih18, dih19, dih20, dih21, dih22, dih23, dih24 }
> colvars: Error: cannot find a colvar named "dih1".
>
>
> The .in file reads (atom ID is given):
>
> colvarsTrajFrequency 100 # output values every 100 steps (default)
> colvarsRestartFrequency 200 # must be > colvarsTrajFrequency
> colvar {
> name dih1 # needed to identify the variable
> width 1.0 # twice the standard deviation during
> # very short simulation; default 1.0
> lowerBoundary -180.0 # lowest end of interval colvar value
> upperBoundary 180.0 # defines the highest possible or allowed value
> outputSystemForce yes # reports also the system force on this
> # colvar in addition to the current value
> dihedral {
> group1 {
> atomNumbers 63 # FE
> }
> group2 {
> atomNumbers 38 # O6
> }
> group3 {
> atomNumbers 36 # C17
> }
> group4 {
> atomNumbers 37 # O5
> }
> }
> colvar {
> name dih2 # needed to identify the variable
> width 1.0 # twice the standard deviation during
> # very short simulation; default 1.0
> lowerBoundary -180.0
> upperBoundary 180.0
> outputSystemForce yes # reports also the system force on this
> # colvar in addition to the current value
> dihedral {
> group1 {
> atomNumbers 63
> }
> group2 {
> atomNumbers 38
> }
> group3 {
> atomNumbers 36
> }
> group4 {
> atomNumbers 33 # C16
> }
> }
> ...................................
> ........................................
> }
> }
> colvar {
> name dih24 # needed to identify the variable
> width 1.0 # twice the standard deviation during
> # very short simulation; default 1.0
> outputSystemForce yes # reports also the system force on this
> # colvar in addition to the current value
> dihedral {
> group1 {
> atomNumbers 59
> }
> group2 {
> atomNumbers 9 # O2
> }
> group3 {
> atomNumbers 18 # O4
> group4 {
> atomNumbers 4 # C3
> }
> }
> }
> harmonic {
>
> name MOL_dihe_harmonic # arbitrary
>
> colvars dih1 dih2 dih3 dih4 dih5 dih6 dih6 dih7 dih8 dih9 dih10 dih11 dih12
> colvars dih13 dih14 dih15 dih16 dih17 dih18 dih19 dih20 dih21 dih22 dih23
> dih24
>
> forceConstant 5.0 # in place of lowerWall upperWall
> }
>
>
> Thanks for help
>
> francesco pietra
>
>

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