Re: ABF error on NAMD 2.10

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Nov 02 2015 - 08:51:52 CST

That information is zero at the first time step for obvious reasons and it
should be updated after writing a restart file.
On Nov 2, 2015 9:45 AM, "Haleh a" <halehabdi_at_sabanciuniv.edu> wrote:

> 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
>>
>>
>>
>

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