Re: Steered MD simulation with pull and rotation

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Apr 02 2018 - 10:40:56 CDT

The NAMD manual, and even the tutorial, would only cover the technical
implementation details. As for what approach is better for your particular
case, you're in charge.

There are a few techniques that are known to be "better" in nearly all
cases (velocity-Verlet time integration, Particle-Mesh Ewald
electrostatics) and are therefore on by default, up to the point that you
may be even unaware of their presence (are you?).

For any biased-MD protocol, some help may come by comparing your case vs.
other published studies. But you do need to understand the theoretical
foundation of each method, and familiarize yourself with the user interface
of each software piece.

Try again the tutorials page, as well as the following:

https://github.com/Colvars/examples

Giacomo

On Mon, Apr 2, 2018 at 10:24 AM, Dhiraj Srivastava <dhirajks_at_gmail.com>
wrote:

> 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
>>
>

-- 
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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