Re: Multi canonical ensemble method

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Oct 30 2019 - 09:22:58 CDT

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

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>
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
>
> 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>
> 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>> 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--0000000000005f3b680596217a86--

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