From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Dec 19 2017 - 18:24:46 CST
Hi Stefano, look closely at the differences between the input files of the
previous run (which did save a PMF file) and the new one, where you only
changed the contents of the .coor file (did you?).
In general, to trigger saving of Colvars output files use the command "cv
save [outputPrefix]", for example right after the "run" command.
Giacomo
On Tue, Dec 19, 2017 at 7:17 PM, Stefano Guglielmo <
stefano.guglielmo_at_unito.it> wrote:
> 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
>> <https://maps.google.com/?q=Via+P.+Giuria+9+%0D+%3E%3E+%3E%3E%3E%3E+10125+Turin,+ITALY+%0D+%3E%3E+%3E%3E%3E%3E+ph.+%2B39&entry=gmail&source=g>
>> >> >>>> 10125 Turin, ITALY
>> <https://maps.google.com/?q=Via+P.+Giuria+9+%0D+%3E%3E+%3E%3E%3E%3E+10125+Turin,+ITALY+%0D+%3E%3E+%3E%3E%3E%3E+ph.+%2B39&entry=gmail&source=g>
>> >> >>>> ph.
>> <https://maps.google.com/?q=Via+P.+Giuria+9+%0D+%3E%3E+%3E%3E%3E%3E+10125+Turin,+ITALY+%0D+%3E%3E+%3E%3E%3E%3E+ph.+%2B39&entry=gmail&source=g>+39
>> (0)11 6707178
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Stefano GUGLIELMO PhD
>> >> >> Assistant Professor of Medicinal Chemistry
>> >> >> Department of Drug Science and Technology
>> >> >> Via P. Giuria 9
>> <https://maps.google.com/?q=Via+P.+Giuria+9+%0D+%3E%3E+%3E%3E+10125+Turin,+ITALY+%0D+%3E%3E+%3E%3E+ph.+%2B39&entry=gmail&source=g>
>> >> >> 10125 Turin, ITALY
>> <https://maps.google.com/?q=Via+P.+Giuria+9+%0D+%3E%3E+%3E%3E+10125+Turin,+ITALY+%0D+%3E%3E+%3E%3E+ph.+%2B39&entry=gmail&source=g>
>> >> >> ph.
>> <https://maps.google.com/?q=Via+P.+Giuria+9+%0D+%3E%3E+%3E%3E+10125+Turin,+ITALY+%0D+%3E%3E+%3E%3E+ph.+%2B39&entry=gmail&source=g>+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
> <https://maps.google.com/?q=Via+P.+Giuria+9+10125+Turin,+ITALY+ph.+%2B39&entry=gmail&source=g>
> 10125 Turin, ITALY
> <https://maps.google.com/?q=Via+P.+Giuria+9+10125+Turin,+ITALY+ph.+%2B39&entry=gmail&source=g>
> ph. +39
> <https://maps.google.com/?q=Via+P.+Giuria+9+10125+Turin,+ITALY+ph.+%2B39&entry=gmail&source=g>
> (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
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