From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Tue Dec 19 2017 - 18:17:35 CST
Hi all,
thanks for your indications.
I re-wrapped and restarted and indeed it is working; anyhow NAMD is not
writing pmf file anymore (all the other files are ok).
What could be the cause?
2017-12-19 19:52 GMT+01:00 Jeff Comer <jeffcomer_at_gmail.com>:
> Thanks, Giacomo. I didn't mean to confuse the issue. I've been in the
> habit of setting colvarsRestartFrequency, when I should probably just
> leave it as the default.
>
> 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 Tue, Dec 19, 2017 at 10:27 AM, Giacomo Fiorin
> <giacomo.fiorin_at_gmail.com> wrote:
> > Hi Jeff, I would be a bit careful with this.
> >
> > It is possible that restartFreq and colvarsRestartFrequency may differ,
> but
> > by default colvarsRestartFrequency is equal to restartFreq. When they
> > differ, it is only because people set them explicitly like that for their
> > own reasons. Because the NAMD restart file does not contain the timestep
> > number, checking this with certainty after the fact will not be possible.
> > If Stefano has the input files he can do so, but I don't know about the
> > general case.
> >
> > On the other hand, the problem of a multi-chain protein "breaking up"
> due to
> > wrapping is a very common scenario. I added the check for "differs
> greatly"
> > after dealing with countless instances of this problem in and out of this
> > mailing list. Fortunately, it is possible to verify whether this is
> > happening. If so, it is also possible to prevent it by disabling
> wrapAll,
> > or by restraining the center-of-mass motion to the molecular complex of
> > interest.
> >
> > Your advice is correct, but it may be misinterpreted by others who just
> want
> > the error message go away.
> >
> > Giacomo
> >
> >
> > On Tue, Dec 19, 2017 at 10:20 AM, Jeff Comer <jeffcomer_at_gmail.com>
> wrote:
> >>
> >> I just wanted to note that the error you're experiencing "differs
> >> greatly from the value last read from the state file" can be due to
> >> the restartFreq in the NAMD configuration file being different from
> >> colvarsRestartFrequency in the Colvars configuration file. The
> >> simulation then starts from a different frame from the last one in the
> >> state file and the value of the colvar is likely to be different. If
> >> this is the reason, one solution is simply to edit the .colvars.state
> >> file and change the value of the colvar to the calculated value
> >> (44.0519).
> >>
> >> 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 Tue, Dec 19, 2017 at 8:08 AM, Giacomo Fiorin
> >> <giacomo.fiorin_at_gmail.com> wrote:
> >> > Hi Stefano, I wouldn't try turning on or off the PBC- and
> >> > wrapping-related
> >> > flags, but try instead to diagnose what is going on.
> >> >
> >> > You could load the same set of input files in VMD:
> >> > mol new *.psf
> >> > mol addfile *.restart.coor
> >> > pbc readxst *.restart.xsc
> >> > (The last one is needed to load the PBC unit cell.) Then load the
> >> > Colvars
> >> > configuration file and evaluate the variables as you did before.
> >> >
> >> > If you conclude that PBC wrapping is to blame, keep in mind that
> >> > disabling
> >> > wrapAll can only prevent future problems. Once the existing restart
> >> > files
> >> > written by NAMD are affected by it, you will probably need to go back
> to
> >> > the
> >> > 2nd most recent set of restart files. Alternatively, you could opt
> for
> >> > translating and re-wrapping your system in VMD using pbctools, or the
> >> > much
> >> > faster qwrap:
> >> > https://github.com/jhenin/qwrap
> >> >
> >> > Then, you can save back the corrected restart file:
> >> > animate write namdbin wrapped.coor
> >> > If you do this you lose the double precision, but it would only be for
> >> > that
> >> > one step when you restart.
> >> >
> >> > Giacomo
> >> >
> >> >
> >> > On Tue, Dec 19, 2017 at 3:48 AM, Stefano Guglielmo
> >> > <stefano.guglielmo_at_unito.it> wrote:
> >> >>
> >> >> Hi Josh and Giacomo,
> >> >> thanks for tips. I tried to re-run tha calculation loading
> >> >> *.restart.colvars.state in the config file, but NAMD is reporting the
> >> >> following error:
> >> >>
> >> >> Error: the calculated value of colvar "distance_ver":
> >> >> colvars: 44.0519
> >> >> colvars: differs greatly from the value last read from the state
> file:
> >> >> colvars: 60.976
> >> >> colvars: Possible causes are changes in configuration, wrong state
> >> >> file,
> >> >> or how PBC wrapping is handled.
> >> >>
> >> >> I double checked the requested files but apparently everything seems
> >> >> correct;
> >> >
> >> >
> >> >
> >> >
> >> >>
> >> >> I also tried with wrapall off and forceNoPBC for the collective
> >> >> variable
> >> >> involved in the error, but the outcome was always the same.
> >> >> Do you have any suggestions?
> >> >> Thanks
> >> >> Stefano
> >> >>
> >> >> 2017-12-19 2:40 GMT+01:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
> >> >>>
> >> >>> If you do have the state file saved, the next run after loading it
> >> >>> should
> >> >>> print the PMF file again.
> >> >>>
> >> >>> Giacomo
> >> >>>
> >> >>> On Dec 18, 2017 7:38 PM, "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov
> >
> >> >>> wrote:
> >> >>>>
> >> >>>> Hi Stefano,
> >> >>>>
> >> >>>> I haven't done it myself, but wouldn't you just need to write a
> >> >>>> script
> >> >>>> to re-add the hills that metadynamics is adding yourself, based
> >> >>>> either on
> >> >>>> the colvars.traj file (ideally) or worst case recalculating your
> >> >>>> reaction
> >> >>>> coordinate trajectory from the dcd? The end result should in
> >> >>>> principle be
> >> >>>> the same if you saved these values at the same frequency that hills
> >> >>>> are
> >> >>>> added, albeit with a large chance of making a mistake somewhere in
> >> >>>> code if
> >> >>>> you don't have a working example to make sure that your script does
> >> >>>> what it
> >> >>>> is supposed to.
> >> >>>>
> >> >>>> -Josh
> >> >>>>
> >> >>>> On 12/18/2017 05:29 PM, Stefano Guglielmo wrote:
> >> >>>> Dear NAMD users,
> >> >>>> is it possible to reconstruct pmf of a metadynamics simulation (if
> >> >>>> for
> >> >>>> some reason the original file was corrupted or lost) in the same
> >> >>>> format as
> >> >>>> the one written as output by NAMD?
> >> >>>> Thanks in advance
> >> >>>> Stefano
> >> >>>>
> >> >>>> --
> >> >>>> Stefano GUGLIELMO PhD
> >> >>>> Assistant Professor of Medicinal Chemistry
> >> >>>> Department of Drug Science and Technology
> >> >>>> Via P. Giuria 9
> >> >>>> 10125 Turin, ITALY
> >> >>>> ph. +39 (0)11 6707178
> >> >>>>
> >> >>>>
> >> >>>>
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Stefano GUGLIELMO PhD
> >> >> Assistant Professor of Medicinal Chemistry
> >> >> Department of Drug Science and Technology
> >> >> Via P. Giuria 9
> >> >> 10125 Turin, ITALY
> >> >> ph. +39 (0)11 6707178
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > 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
> >
> >
> >
> >
> > --
> > 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
>
-- Stefano GUGLIELMO PhD Assistant Professor of Medicinal Chemistry Department of Drug Science and Technology Via P. Giuria 9 10125 Turin, ITALY ph. +39 (0)11 6707178
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