Re: reconstructing pmf

From: Giacomo Fiorin (
Date: Tue Dec 19 2017 - 08:08:03 CST

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:

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.


On Tue, Dec 19, 2017 at 3:48 AM, Stefano Guglielmo <> 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 <>:
>> 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" <>
>> 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
>>> <,+ITALY+%0D+ph.+%2B39&entry=gmail&source=g>
>>> 10125 Turin, ITALY
>>> ph. +39 (0)11 6707178
> --
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> <,+ITALY+%0D+ph.+%2B39&entry=gmail&source=g>
> 10125 Turin, ITALY
> <,+ITALY+ph.+%2B39&entry=gmail&source=g>
> ph. +39
> <,+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

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