From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Tue Dec 23 2014 - 15:59:09 CST
I think Jeff is right and after each group4 there should be 3 closing brackets, not two.
Though, I haven’t checked that.
Maxim
> On Dec 23, 2014, at 15:35, Jeff Comer <jeffcomer_at_gmail.com> wrote:
>
> 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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