Re: Re: metadynamics run in NAMD or using plumed in NAMD

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Dec 08 2017 - 12:19:43 CST

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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