From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Fri Dec 08 2017 - 12:14:11 CST
Dear Mr. Giacomo,
Thank you very much. I have tried to analyze metadynamics trajectories from
NAMD run in META-GUI. After modifying the title of the colvar and hills
file, it looks like working. It can calculate "FIND MICROSTATES", "COMPUTER
FREE ENERGY", "DIAG KINETIC MATRIX", but I am getting one error while
calculating KINETIC BASIN-
couldn't open "BASINS_RUN/CLUSTERS.BASINS.ALL_EIGENVECTORS": no such file
or directory
couldn't open "BASINS_RUN/CLUSTERS.BASINS.ALL_EIGENVECTORS": no such file
or directory
while executing
"open "$EIGENVECTORS_folder/CLUSTERS.BASINS.ALL_EIGENVECTORS" r"
(procedure "build_basins" line 35)
invoked from within
"build_basins $NUMBER_of_VECTORS $KT_RANGE"
invoked from within
".metagui.out1.cbas.run.b invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .metagui.out1.cbas.run.b"
(command bound to event)
I will be grateful if you can help me with this.
Thanks very much.
Rabeta Yeasmin
On Fri, Dec 8, 2017 at 7:08 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> META-GUI is largely based on the use of the files COLVAR and HILLS, or
> similar names. The former is named <outputName>.colvars.traj in Colvars,
> the latter is called <outputName>.metadynamics.hills.traj and you can
> enable it by the writeHillsTrajectory keyword.
>
> Details are available here:
> http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:
> colvarbias_meta
>
> Giacomo
>
> On Fri, Dec 8, 2017 at 3:06 AM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
> wrote:
>
>> Dear all,
>>
>> Thank you very much for all of your information. I am wondering if I can
>> run bias-exchange metadynamics on NAMD using colvar module and how can I
>> analyze results of metadynamics. In the tutorial, they had shown plotting
>> pmf. But if I want to find the kinetic basins, how can I get it.
>> I have found one program META-GUI for analyzing metadynamics results
>> which is based on plumed output version. I am wondering if I can that
>> program to analyze metadynamics from NAMD.
>>
>> Rabeta Yeasmin
>>
>> On Thu, Dec 7, 2017 at 5:49 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
>> wrote:
>>
>>> Dear NAMD users,
>>>
>>> I am trying to run metadynamics in NAMD. I have searched online for
>>> related information. I have found one tutorial in NAMD tutorial and also
>>> found something like-running metadynamics using plumed version- in NAMD
>>> version-. I am wondering if these two methods are same or not. If yes, how
>>> am I going to use plumed with NAMD.
>>>
>>> Thanks.
>>>
>>> Rabeta Yeasmin
>>>
>>
>>
>
>
> --
> 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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