From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Fri Dec 08 2017 - 12:39:49 CST
Thanks very much. Hope to hear something from Mr. Toni soon.
Rabeta Yeasmin
On Fri, Dec 8, 2017 at 12:19 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> This is a question for the META-GUI developers. Copying here Toni,
> developer of the latest version.
>
> On Fri, Dec 8, 2017 at 1:14 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
> wrote:
>
>> 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
>>>
>>
>>
>
>
> --
> 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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