From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Sep 20 2012 - 12:45:49 CDT
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
>> > }
>> >
>> > Thank you in advance, for your time and consideration in answering my
>> > query.
>> >
>> > regards,
>> > Nabaneeta
>> >
>
>
>
>
> --
> ..................................
> ''Vidya Dadati Vinayam''
> Knowledge gives humility
>
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