Re: ABF simulation with extendedLagrangian on keeps crashing

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue May 03 2011 - 08:11:26 CDT

Hi,

I tried that, but it still crashes. I'll try to reduce the integration step
even further (to 0.5 or 0.2 fs) and play around with temperature control
(perhaps disable it).

A while ago I boasted, that I will try to derive the analytical derivative
for the angle colvar, but even after pulling in a couple of
theoretical physicists we failed miserably. It would take me (us) too much
time to grasp the basic concepts and the maths behind ABF.

Best regards,
Ajasja

On Fri, Apr 22, 2011 at 22:38, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:

> Hi Ajasja,
>
> Just a guess, but the force constants for the walls are a tad high.
> You may want to try something on the order of 1, especially if the
> crashes happen near the boundaries.
>
> Jerome
>
> On 22 April 2011 16:27, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com> wrote:
> >>
> >> I'll try running two 1D simulations, just to see if this works better.
> >
> > It's the angle colvar (theta) that is blowing up.
> > Is there anything particularly illegal in this colvar?
> > colvar {
> > name theta
> > width 5
> > lowerboundary 0
> > upperboundary 180
> > lowerWallConstant 10
> > upperWallConstant 10
> >
> > extendedLagrangian on
> >
> > angle {
> >
> > group1 { dummyAtom (3.283, -0.213, 99.366) } ; #100 Ang above CB
> > group2 { atomnumbers 204 } ;#CB
> > group3 { atomnumbers 173 } ;#O1
> > }
> > }
> >
> > Thank you & best regards,
> >
> > Ajasja
>

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