Re: ABF simulation with extendedLagrangian on keeps crashing

From: JťrŰme Hťnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu May 05 2011 - 10:23:23 CDT

Hi Ajasja,

Your crashes might come from the singularity that occurs if one of the
actual atoms gets too close with the dummy atom.

As promised, I have just implemented ABF-specific routines for the
angle component. I've only had time for very basic testing though. It
looks fine, but it would be best if you can try it on a trivial system
first. The two source files attached should be sufficient to enable
it.

Cheers,
Jerome

On 5 May 2011 10:38, Ajasja Ljubetińć <ajasja.ljubetic_at_gmail.com> wrote:
> Hi,
>
> I gave up on ABF for the time being and ran a metadynamics simulation. But
> the simulation still crashed, although I did not see anything in the
> trajectory even when writing every step.
> The colvar traj is shown
> here<http://www.ijs.si/ijs/dept/epr/ajasja/mails/ABF/meta-theta-crash.png>.
> I'll try to somehow get rid of the dummy atom and see if it runs better.
>
> Best regards,
> Ajasja
>
>
>
> colvarsTrajFrequency 1
> colvarsRestartFrequency 1000
> colvar {
>  name theta
>
>  width 5
>  lowerboundary 0
>  upperboundary 180
>  lowerWallConstant 1
>  upperWallConstant 1
>
>
>
>  angle {
>
>    group1 { dummyAtom (3.283, -0.213, 99.366) } ;
>    group2 { atomnumbers 204 } ;#CB
>    group3 { atomnumbers 173 } ;#O1
>
>  }
> }
>
> colvar {
>  name phi
>
>  width 5
>  lowerboundary -90
>  upperboundary +90
>  lowerWallConstant 1
>  upperWallConstant 1
>
>
>
>  dihedral {
>
>    group1 { atomnumbers 173 } ;#O1
>    group2 { atomnumbers 204 } ;#CB
>    group3 { dummyAtom (3.283,  -0.213, -100.63) } ;
>    group4 { dummyAtom (13.283, -0.213, -100.63) } ;
>  }
> }
>
>
>
> metadynamics {
>  name CAO_T
>  colvars theta
>  hillWeight 0.05
>  newHillFrequency 100
> }
>
>
> histogram {
>   name CBO_TP_hist
>   colvars theta phi
> }
>
> On Wed, May 4, 2011 at 13:31, Ajasja Ljubetińć <ajasja.ljubetic_at_gmail.com>wrote:
>
>> Hi,
>>
>> I checked the crash in more detail:
>> http://www.ijs.si/ijs/dept/epr/ajasja/mails/ABF/bouncing.png
>> It looks like the colvar is at the same time attracted to the upper
>> boundary and bounces of it.
>>
>> Here the ABF bias was only active for the theta colvar (the angle colvar)


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