From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Sep 20 2012 - 11:59:47 CDT
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
>
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