Re: Multi canonical ensemble method

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Nov 05 2019 - 07:18:49 CST

Hello Takeru, please keep the list in CC.

Your error is due to using curly braces instead of parentheses.

Giacomo

On Mon, Nov 4, 2019 at 9:39 PM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp>
wrote:

> Dear Giacomo
>
> Thank you for your kind reply.
>
> I tried ABF as you said using attached files.
>
> However, I obtained attached log file (run.log).
>
> Are there any missing configurauin ?
>
> Thanks
>
> Best wishes,
> Takeru Kameda
> PhD Student, Hiroshima University, Japan
>
> ________________________________________
> 差出人: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> 送信日時: 2019年10月30日 23:22
> 宛先: Takeru KAMEDA
> CC: Jérôme Hénin; namd-l
> 件名: Re: namd-l: Multi canonical ensemble method
>
> Hello Takeru, it looks like you already found the documentation, try to
> double-check that your configuration is consistent. See here an example:
> https://raw.githubusercontent.com/Colvars/colvars/master/tests/spinangle.in
> <
> https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FColvars%2Fcolvars%2Fmaster%2Ftests%2Fspinangle.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187028882&sdata=uDrPerxN1ceCjrQhZ4yfQ9Qpp3xln2AQwhnE4Cs%2B5ak%3D&reserved=0
> >
>
> If it is consistent with the doc, do you mind pasting it in the email or
> attaching it?
>
> Giacomo
>
> On Wed, Oct 30, 2019 at 1:28 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp
> <mailto:kamedapon_at_hiroshima-u.ac.jp>> wrote:
> Hi Jerome.
>
> Thank you for your advice.
> And, sorry for the late reply.
>
>
> I changed the method orientation to spinAngle.
> https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html#24897<
> https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.13%2Fug%2Fnode55.html%2324897&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187028882&sdata=XY27Nbbf20n3dSyNa%2BJOc7key7RYeJHD3602iGzuaMU%3D&reserved=0
> >
>
> Now I'm trying such method.
> However, I can not set "axis" part in "List of keywords" of spinAngle.
>
> In this case, I think I must set the axis of rotation and center of
> roration.
>
> Do you know how to set such axis and center.
>
>
> Best wishes,
> Takeru Kameda
> PhD Student, Hiroshima University, Japan
>
> ________________________________________
> 差出人: Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>>
> 送信日時: 2019年9月30日 20:49
> 宛先: Takeru KAMEDA
> CC: namd-l
> 件名: Re: namd-l: Multi canonical ensemble method
>
> Dear Takeru,
>
> this "failed dependency" message indicates that ABF only supports scalar
> variables. A multidimensional ABF calculation can be done with several
> scalar variables, not a single vector one.
>
> In this case, the orientation variable is 4-dimensional, which is probably
> too much for ABF anyway. I recommend reducing your sampling space to 1, 2
> or 3 scalar quantities.
>
> Best wishes,
> Jerome
>
> On Mon, 30 Sep 2019 at 04:23, Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp
> <mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp
> <mailto:kamedapon_at_hiroshima-u.ac.jp>>> wrote:
> Dear all.
>
> Hi. I am trying multi-canonical ensemble method using NAMD2.13.
>
> I wrote colvar file as follows:
>
> colvarsTrajFrequency 5000
> colvarsRestartFrequency 50000
>
> colvar {
> name theta
>
> outputValue on
> #outputVelocity on
> #outputEnergy on
> #outputSystemForce on
> #outputAppliedForce on
>
> orientation {
> atoms { atomnumbers {
> 13754 13755 13756 13757 13758 13761 13783 13785 19290
> 19291 19292 19293 19294 19297 19319 19321
> }}
> refPositionsFile ./colvar.pdb
> refPositionsCol O
> }
> }
>
> abf {
> colvars theta
> fullSamples 200
> hideJacobian
> }
>
>
> Then, we execute simulation, following error was output:
>
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 2018-10-16--0000000000002f66d00596994b6e--

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