Re: Steered MD simulation with pull and rotation

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Mon Apr 02 2018 - 09:24:36 CDT

Thanks Giacomo
                            I was trying to read and understand about it
but little bit confused about colvar and rotation force in namd. Which one
is better? Is there any manual/review article/book that can help me better
understand these things? I tried to search for it but can not find any
except the manuals available through namd which is not very good in
teaching basics.

Thanks
Dhiraj

On Thursday, March 29, 2018, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hello Dhiraj, it sounds like you could achieve this with a combination of
> the distanceZ and spinAngle collective variables:
> http://colvars.github.io/colvars-refman-namd/colvars-
> refman-namd.html#sec:cvc_distanceZ
> http://colvars.github.io/colvars-refman-namd/colvars-
> refman-namd.html#sec:cvc_spinAngle
>
> with a moving harmonic restraint acting on both.
>
> Giacomo
>
> On Wed, Mar 28, 2018 at 3:23 PM, Dhiraj Srivastava <dhirajks_at_gmail.com>
> wrote:
>
>> Hi all
>> I want to do simulation of my protein where I want to pull out a
>> helix and rotate it simultaneously. is it possible to do it in NAMD or I
>> have to do one at a time? also, is there any tutorial or example for such
>> kind of simulation, specially both at the same time or rotation?
>>
>> Thank you
>> Dhiraj
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

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