Re: ABF error on NAMD 2.10

From: Haleh a (halehabdi_at_sabanciuniv.edu)
Date: Mon Nov 02 2015 - 08:45:29 CST

It worked when I corrected for the end of line characters. Thank you.
However, I still do not understand why I get abf.pmf and Abf.colvar.state
files with all zeros and they do not get updated at every step.

 abf.pmf file:

  xi A(xi)
       0.1 0
      0.15 0
       0.2 0
      0.25 0
       0.3 0
      0.35 0
       0.4 0
      0.45 0
       0.5 0
      0.55 0
       0.6 0
      0.65 0
       0.7 0
      0.75 0
       0.8 0
      0.85 0
       0.9 0
      0.95 0
         1 0
      1.05 0
       1.1 0
      1.15 0
       1.2 0
      1.25 0

and

Abf.colvar.state

configuration {
  step 1104000
  dt 1.00000000000000e+000
}

colvar {
  name RMSD
  x 1.56341258634097e+000
}

abf {
  configuration {
    name abf1
  }
samples
 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0

gradient
 0 0 0
 0 0 0
 0 0 0
 0 0 0
 0 0 0
 0 0 0
 0 0 0
 0 0
}

On Mon, Nov 2, 2015 at 3:49 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Haleh, the colvars version 2012-03-23 is not part of NAMD 2.10. It was
> bundled instead with 2.9. Please double-check the version you are running.
>
> You may also want to make sure you are writing the config file (a text
> file) on the same platform you want to run: Windows and Linux have
> different terminal characters for end of line.
>
> On Mon, Nov 2, 2015 at 6:55 AM, Haleh a <halehabdi_at_sabanciuniv.edu> wrote:
>
>> Dear NAMD users,
>>
>> Recently, I have been trying to run ABF simulations with RMSD as the
>> collective variables. I am using the following *.in file:
>>
>> #rmsd.in
>> Colvarstrajfrequency 1000
>> Colvarsrestartfrequency 1000
>> colvar {
>> name RMSD
>> width 0.05
>> lowerboundary 0.1
>> upperboundary 1.25
>> lowerwallconstant 100.0
>> upperwallconstant 100.0
>> outputAppliedForce on
>>
>> rmsd {
>> atoms {
>> psfSegID P1
>> atomNameResidueRange CA 1-159
>> atomsFile main_abf.pdb
>> atomsCol B
>> atomsColValue 1.0
>> }
>> refPositionsFile ref_abf.pdb
>> refPositionsCol B
>> refPositionsColValue 1.0
>> }
>> }
>>
>> abf {
>> colvars RMSD
>> fullSamples 1000
>> }
>>
>> I am getting the following error on NAMD 2.10 on a cluster :
>>
>> colvars:
>> ----------------------------------------------------------------------
>> colvars: Initializing the collective variables module, version 2012-03-23.
>> colvars: # analysis = off [default]
>> colvars: # colvarsTrajFrequency = 1000
>> colvars: # colvarsRestartFrequency = 1000
>> colvars: # colvarsTrajAppend = off [default]
>> colvars: The restart output state file will be "abf.colvars.state".
>> colvars: The final output state file will be "abfo.colvars.state".
>> colvars: The trajectory file will be "abfo.colvars.traj".
>> colvars:
>> ----------------------------------------------------------------------
>> colvars: Initializing a new collective variable.
>> colvars: # name = RMSD
>> colvars: Initializing a new "rmsd" component.
>> colvars: # componentCoeff = 1 [default]
>> colvars: # componentExp = 1 [default]
>> colvars: # period = 0 [default]
>> colvars: # wrapAround = 0 [default]
>> colvars: Error: definition for atom group "atoms" not found.
>> colvars: If this error message is unclear, try recompiling with
>> -DCOLVARS_DEBUG.
>> FATAL ERROR: Error in the collective variables module: exiting.
>>
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Error in the collective variables module: exiting.
>>
>>
>> I tried running the same script on NAMD 2.9 on my desktop. It does not
>> give me the same error. However, my Abf.colvar.state and abf.pmf files are
>> empty as follows:
>>
>> abf.pmf file:
>>
>> xi A(xi)
>> 0.1 0
>> 0.15 0
>> 0.2 0
>> 0.25 0
>> 0.3 0
>> 0.35 0
>> 0.4 0
>> 0.45 0
>> 0.5 0
>> 0.55 0
>> 0.6 0
>> 0.65 0
>> 0.7 0
>> 0.75 0
>> 0.8 0
>> 0.85 0
>> 0.9 0
>> 0.95 0
>> 1 0
>> 1.05 0
>> 1.1 0
>> 1.15 0
>> 1.2 0
>> 1.25 0
>>
>>
>> and
>>
>> Abf.colvar.state
>>
>> configuration {
>> step 1104000
>> dt 1.00000000000000e+000
>> }
>>
>> colvar {
>> name RMSD
>> x 1.56341258634097e+000
>> }
>>
>> abf {
>> configuration {
>> name abf1
>> }
>> samples
>> 0 0 0 0 0 0 0 0
>> 0 0 0 0 0 0 0 0
>> 0 0 0 0 0 0 0
>>
>> gradient
>> 0 0 0
>> 0 0 0
>> 0 0 0
>> 0 0 0
>> 0 0 0
>> 0 0 0
>> 0 0 0
>> 0 0
>> }
>>
>> Any suggestion to remove the error and help me get more clear on the
>> subject is highly appreciated.
>>
>>
>> Best regards,
>> Haleh
>>
>
>
>
> --
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
> http://goo.gl/Q3TBQU
> http://giacomofiorin.github.io/
> https://icms.cst.temple.edu/members.html
>
>
>

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:22:12 CST