From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Wed Apr 03 2019 - 09:55:00 CDT
Dear Jeff and Giacomo,
Thanks, a lot for explaining things, it is more clear now.
Thanks and regards
Abhi
________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Wednesday, April 3, 2019 1:02:25 AM
To: NAMD list; Jeff Comer
Cc: Abhishek TYAGI
Subject: Re: namd-l: inputPrefix merge error ABF
FYI as Jeff explained by default NAMD will switch its working directory to the parent directory of the given configuration file, regardless of where it's being called from.
However, you can use namd2 --source <path_to_config_file> to just read the config file, but not switch to that file's parent directory. This should allow you to read the configuration from a file anywhere on the file system, but keep working in the same directory where you launch NAMD.
http://www.ks.uiuc.edu/Research/namd/2.13/ug/node9.html
Giacomo
On Tue, Apr 2, 2019 at 12:05 PM Jeff Comer <jeffcomer_at_gmail.com<mailto:jeffcomer_at_gmail.com>> wrote:
Dear Abhi,
The new .hist.grad files and .hist.count files are a continuation of
the evolution of the ABF bias, in the same way that the DCD files are
a continuation of the trajectory of the coordinates. Your new DCD is
initially smaller than the previous DCD file. Your new .hist.grad and
.hist.count files are analogously smaller than the previous .hist.grad
and .hist.count files.
All of the information necessary for the current and future
application of the ABF method are included in the count (.count) and
gradient (.grad) files. The count is the number of samples in each bin
along the reaction coordinate and the gradient is the mean force on
the reaction coordinate for each of these bins. When you use
inputPrefix, ABF uses these count and gradient files to set the
initial state and starts accumulating new samples from there.
Internally, the Colvars code stores a "count" grid and a "sum of force
samples" grid (count_i * gradient_i). The entire history of force
samples at each step (ξ_s, F(ξ_s)) is not stored, nor is the history
of the evolution of the count and gradient grids stored (except if you
specify a historyFreq and write the .hist.count and .hist.grad files).
As I see it, the .hist.grad and .hist.count files are only useful for
convergence analysis and statistical analysis of your free energy
calculation.
I hope that helps to clarify what is going on.
Regards,
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
Website: http://jeffcomer.us
On Mon, Apr 1, 2019 at 10:29 PM Abhishek TYAGI <atyagiaa_at_connect.ust.hk<mailto:atyagiaa_at_connect.ust.hk>> wrote:
>
> Dear Jeff,
>
>
> Thanks for the reply and your suggestion worked perfectly when I put *.count and *.grad files in the same folder as of namd conf file.
>
>
> I have a stupid question, I am not sure why this is happening:
>
> The new data obtained for pmf, hist.pmf hist.grad .. etc, have numbers inside, however, I noticed that the file size is far smaller than the earlier files from the same MD, as I have used inputprefixto combine them.
>
>
> Thanks and regards
>
> Abhi
>
>
> ________________________________
> From: Jeff Comer <jeffcomer_at_gmail.com<mailto:jeffcomer_at_gmail.com>>
> Sent: Tuesday, April 2, 2019 4:36:02 AM
> To: NAMD list; Abhishek TYAGI
> Subject: Re: namd-l: inputPrefix merge error ABF
>
> Are you sure that solvate_ua+ions.3.count is present in the NAMD
> working directory? You should note that the position of the file given
> in the Colvars configuration file is relative to the directory that
> NAMD is called from, not the directory that the Colvars configuration
> file is in.
>
> 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
> Website: http://jeffcomer.us
>
> On Sun, Mar 31, 2019 at 11:48 PM Abhishek TYAGI <atyagiaa_at_connect.ust.hk<mailto:atyagiaa_at_connect.ust.hk>> wrote:
> >
> > Dear Experts,
> >
> >
> > After finishing ABF calculations, I need to combine them for post-processing of data. I have used inputPrefix to combine the files, but I have faced error as shown below. (I am using NAMD_2.13)
> >
> >
> > The keyword were set in the colver input file:
> >
> >
> > abf {
> > colvars NormalMolMem
> > fullSamples 500
> > historyFreq 20000
> > updateBias no
> > inputPrefix solvate_ua+ions.3 solvate_ua+ions.4 solvate_ua+ions.5 solvate_ua+ions.6 solvate_ua+ions.7
> > }
> >
> > Error in log file as follows:
> >
> >
> > colvars: Collective variables initialized, 1 in total.
> > colvars: ----------------------------------------------------------------------
> > colvars: Initializing a new "abf" instance.
> > colvars: # name = "abf1" [default]
> > colvars: # colvars = { NormalMolMem }
> > colvars: # outputEnergy = off [default]
> > colvars: # timeStepFactor = 1 [default]
> > colvars: # applyBias = on [default]
> > colvars: # updateBias = off
> > colvars: WARNING: ABF biases will *not* be updated!
> > colvars: # hideJacobian = off [default]
> > colvars: Jacobian (geometric) forces will be included in reported free energy gradients.
> > colvars: # fullSamples = 500
> > colvars: # inputPrefix = { solvate_ua+ions.3, solvate_ua+ions.4, solvate_ua+ions.5, solvate_ua+ions.6, solvate_ua+ions.7 }
> > colvars: # outputFreq = 20000 [default]
> > colvars: # historyFreq = 20000
> > colvars: # shared = off [default]
> > colvars: # maxForce = [default]
> > colvars: # integrate = on [default]
> > colvars: Reading sample count from solvate_ua+ions.3.count and gradient from solvate_ua+ions.3.grad
> > colvars: Error opening ABF samples file solvate_ua+ions.3.count for reading
> > FATAL ERROR: Error in the collective variables module: No such file or directory
> >
> >
> > The colvarsConfig file is placed in the same folder with the other files, still can't find the files, though the files are next to the input files, I am sure the path is correct
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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