# Re: using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion

From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Sep 20 2012 - 12:58:35 CDT

Just to clarify on the degrees of freedom question. If you restrain say
the rotations and two of the translations you are interested in, and just
pull across the last dimension, your PMF will be perfectly accurate, for
examining that particular case (i.e. the energy landscape of the motion
along just that dimension).

If you think that is the major contributor to the free energy, then it is a
good assumption. If, however, there are a number of other configurations
which may contribute nearly the same energy, you might get misleading

If you don't use the restraints, the amount of simulation time needed to
sample enough to get a converged answer will likely be extreme. A good
thing to do (I'm not saying this is the best) is to restrain those other
degrees of freedom within some manageably small range, using a flat-bottom
restraint (in the case of the colvar, this means a harmonic restraint with
no force constant, but upper and lower walls and associated constants).

One final thing, if you're just starting in on these kind of calculations,
I would strongly recommend using the Metadynamics method of the colvars
module. It gives the same answer as Umbrella sampling, but is more
automated and easier to setup. It has some disadvantages over Umbrella
sampling, but in terms of quickly getting a rough answer for the energy
landscape, it is extremely effective.

~Aron

On Thu, Sep 20, 2012 at 1:45 PM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:

> You are mentioning translations, but there are also rotations. A
> system of two rigid bodies has twelve degrees fo freedom, six of which
> are internal.
>
> With the colvars module, you can restrain all of them in various ways.
> And yes, these restraints will contribute to the PMF, so you need to
> think carefully of what process exactly you are trying to model.
>
> Jerome
>
>
> On 20 September 2012 19:05, nabaneeta mukhopadhyay
> <nabaneeta85_at_gmail.com> wrote:
> > Thanks a lot.
> > Speaking of other degrees of freedom of the nanotubes, I haven't put any
> > constraints on them. Is there a way so that I can restrict their motion
> > along the y and z axis so that they only move along x-axis. If so, will
> that
> > force also contribute to the PMF?
> >
> > Thanks and regards,
> > Nabaneeta
> >
> >
> > On Thu, Sep 20, 2012 at 10:29 PM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr
> >
> > wrote:
> >>
> >> Hi Nabaneeta and everyone,
> >>
> >> First I need to make a comment, just for the record. I said somewhere
> >> in the documentation that you could use this staged pulling protocol
> >> to do Umbrella Sampling. What I certainly never said anywhere is that
> >> doing so was a good idea. I mean, generally speaking.
> >>
> >> To answer your specific question, my guess is that it could work,
> >> provided that you take care of the other degrees of freedom of the
> >> nanotubes.
> >>
> >> All the best,
> >> Jerome
> >>
> >>
> >> On 20 September 2012 18:21, nabaneeta mukhopadhyay
> >> <nabaneeta85_at_gmail.com> wrote:
> >> > Hello Everyone,
> >> >
> >> > My system consists two single wall carbon nanotubes in aqueous
> >> > dispersion.
> >> > Each tube consists 260 atoms. I want to calculate PMF of the system
> >> > using
> >> > Umbrella Sampling technique by varying separations (7-18 angstrom)
> along
> >> > x-axis between the two tubes. I am applying a harmonic potential of
> >> > force
> >> > constant = 0.5
> >> >
> >> > I start at a separation of 18 angstrom between the tubes and then
> >> > eventually
> >> > decrease the separation along x-axis (17, 16 , 15,........,7
> angstrom).
> >> > Simulation time at each step is is 1 ns.
> >> > I am going to use colvar for umbrella sampling purpose. For that I
> have
> >> > prepared the input file given below. I am a newbie in this field and
> >> > I'll
> >> > really appreciate if someone can let me know whether this is a correct
> >> > method or not.
> >> >
> >> > # colvar config file
> >> > #output values every 100 steps
> >> > colvarsTrajFrequency 100
> >> >
> >> > colvar{
> >> > name colvar_dist
> >> > OutputSystemForce yes
> >> >
> >> > distance
> >> > {
> >> > group1
> >> > {
> >> > atomNumbersRange 1-260
> >> > }
> >> > group2
> >> > {
> >> > atomNumbersRange 261-520
> >> > }
> >> > }
> >> > }
> >> >
> >> > harmonic
> >> > {
> >> > name potential
> >> > colvars colvar_dist
> >> > centers 18.0
> >> > targetCenters 18.0 17.0 16.0 15.0 14.0 13.0 12.0 11.0 10.0 9.0 8.0
> >> > targetNumsteps 10000000
> >> > targetNumStages 11
> >> > force constant 0.5
> >> > }
> >> >
> >> > query.
> >> >
> >> > regards,
> >> > Nabaneeta
> >> >
> >
> >
> >
> >
> > --
> > ..................................
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