From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu May 05 2011 - 03:38:16 CDT
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)--000e0cd6b2de6efc6c04a2834b1b--
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