From: Hadi (dinpajooh_at_gmail.com)
Date: Wed Aug 06 2014 - 16:07:27 CDT
I do not see any difference between NAMD and all other MD codes which use
"bond constraint" algorithms to incorporate rigid bodies. Therefore, this
discussion does not pertain to "one" MD code. This pertains to all MD codes
which use similar methods/algorithms and the original question was related
to these algorithms and not the ones you mention. So I think I did not
generalize it more than this.
On Wed, Aug 6, 2014 at 1:48 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Wed, Aug 6, 2014 at 4:40 PM, Hadi <dinpajooh_at_gmail.com> wrote:
> > Axel,
> > This discussion is in NAMD list and it is about rigid models which use
> > constraints. I do not want to generalize it more than this.
> but you *do*. it doesn't matter what you *want*. NAMD is one
> implementation of MD and thus talking about MD as a general method is
> just as applicable than talking about the specific MD implementation
> that is NAMD. thus when you say "in NAMD" than this refers to NAMD as
> the MD implementation, if you write "in MD" however you are referring
> to MD as the method in general and not just NAMD.
> i strongly suggest you keep this in mind for future discussions. on
> mailing lists, with colleagues or in publications. anywhere.
> > Thanks,
> > Hadi
> > On Wed, Aug 6, 2014 at 1:28 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> >> On Wed, Aug 6, 2014 at 3:41 PM, Hadi <dinpajooh_at_gmail.com> wrote:
> >> > In Monte Carlo, you do not need to use a constraint solver to
> >> > the
> >> > rigid models. This is what I like to emphasize: unlike MD, they can
> >> > "easily"
> >> > be implemented. There is no need to solve a constraint. So I think you
> >> > are
> >> no. no. no. please pay attention. in MD you can do rigid bodies
> >> without constraints just as well and instead of solving constraints.
> >> you just propagate the center of mass and the rotational degrees of
> >> freedom. this works very well, and i am using it regularly. it just
> >> isn't implemented in NAMD but it is available in many other MD codes.
> >> in fact, there are MD codes that *only* support such rigid body
> >> propagators and do not have a constraint solver at all.
> >> > mistaken: "the difference you were referring to is the difference
> >> > between a
> >> > rigid body propagator and using a constraint solver and that has
> >> > to
> >> > do with MD vs. MC."
> >> no. i stand by this sentence. you seem to be forgetting that NAMD is
> >> not every MD program.
> >> > I agree the term rigid model used in this thread is the one which uses
> >> > the
> >> > bond constraints and the discussions pertain to the corresponding
> >> > methods.
> >> again, you are missing the point i am criticizing. it is not what the
> >> discussion started with that i have an issue with, but your wholly
> >> unjustified, unproven, and incorrect generalizations.
> >> axel.
> >> > Thanks a lot for your comments.
> >> > Hadi
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> College of Science & Technology, Temple University, Philadelphia PA, USA
> >> International Centre for Theoretical Physics, Trieste. Italy.
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
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