From: Jrme Hnin (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 Ljubetič <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 Ljubetič <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)
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:04 CST
