From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Dec 19 2017 - 12:52:21 CST
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
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