From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Tue Dec 19 2017 - 02:48:53 CST
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
Error: the calculated value of colvar "distance_ver":
colvars: differs greatly from the value last read from the state file:
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?
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.
> On Dec 18, 2017 7:38 PM, "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov>
>> 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.
>> 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 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
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