Re: Equilibration when splitting an ABF calculation

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Jan 28 2011 - 06:26:58 CST

Dear Jerome,

The pulling <http://img10.imageshack.us/img10/5561/abfpulling.png> went OK,
the equilibration <http://img545.imageshack.us/img545/5890/abfrelax.png> as
well. The ABF <http://img228.imageshack.us/img228/7672/abfh.png>is
running smoothly, only do you think I would I need a higher wall
constant? Some points are outside the regions, but since the wall potential
is a harmonic potential, there are always some points outside the region,
right?

Best regards,
Ajasja

On Thu, Jan 27, 2011 at 15:48, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>wrote:

> Dear Jerome,
>
>
> >Even simpler: you can enable the colvars, including their wall
> >potentials, but not ABF (e.g. comment out the abf block).
>
> Aha, so the upper and lower wall potentials are active as soon as a colvar
> is defined? That's good to know, thanks.
>
> Best regards,
> Ajasja
>
> On Thu, Jan 27, 2011 at 15:08, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
>
>> Hi Ajasja,
>>
>> On 27 January 2011 13:25, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
>> wrote:
>> > Dear all,
>> > I partitioned the FES of my system into eight smaller parts. For each
>> part I
>> > wanted the system to be inside the region of interest (ROI) when
>> starting
>> > the calculation, so puled the each part to the desired location (using
>> the
>> > harmonic keyword of the colvars module - fig I). I then slowly relaxed
>> > the constraint and let each part equilibrate for a while. For some parts
>> the
>> > system escaped from the ROI during equlibration (fig II - at least F and
>> B
>> > are out of ROI). So when the ABF simulation started the system was not
>> > inside the boundaries defined for the colvars for some parts.
>> > Two questions:
>> >
>> > Is this a problem? When the ABF started the wall potential will push the
>> > system to the right region, but probably with some input of energy.
>>
>> Indeed, and that defeats the purpose of equilibrating before that...
>>
>> > How could I have ensured the the system stays in the ROI during
>> > equlibration? Should I have ABF turned on during equilibration, but with
>> a
>> > very high fullsamples, so only the wall potential is active?
>>
>> Even simpler: you can enable the colvars, including their wall
>> potentials, but not ABF (e.g. comment out the abf block).
>>
>> Cheers,
>> Jerome
>>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:32 CST