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

From: nabaneeta mukhopadhyay (nabaneeta85_at_gmail.com)
Date: Thu Sep 20 2012 - 12:05:49 CDT

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
> > }
> >
> > Thank you in advance, for your time and consideration in answering my
> query.
> >
> > regards,
> > Nabaneeta
> >
>

-- 
..................................
''Vidya Dadati Vinayam''
Knowledge gives humility

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:06 CST