From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Aug 07 2014 - 10:50:24 CDT
OK, have it your way. Axel and I are to blame for misunderstanding you
because we are oblivious to the real-life concerns of MD usage and
development, everything you posted was done knowingly and deliberately,
and nothing you did was based on incomplete knowledge of the subject
matter. This, however, implies you knowingly and deliberately tried to
mislead Viswanath Pasumarthi into running a flexible simulation using the
"fallback" TIP3P parameters in the CHARMM force field distribution, rather
than applying RigidBonds. Now guess who I'd have the least respect for,
the guy who knows everything and cynically tries to mislead others, or the
guy who tries to help others but accidentally gives an incorrect pointer
because of not knowing everything?
On 08/06/2014 06:39 PM, Hadi wrote:
> I am sorry you misunderstood my statements.
> Have a good day!
> Hadi
>
>
> On Wed, Aug 6, 2014 at 3:28 PM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>
> *facepalm* Dude, just admit you made an incorrect generalization and
> let it go. You might be from a culture where it's shameful to admit a
> mistake, but you're in a scientific community here, where nobody knows
> everything and stuff is falsified all the time because everyone is
> looking to falsify others' results. Being wrong is normal here, and
> what's shameful is failing to admit one's mistakes.
>
>
>
> On 08/06/2014 05:07 PM, Hadi wrote:
>
> 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.
> Hadi
>
>
> On Wed, Aug 6, 2014 at 1:48 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> <mailto:akohlmey_at_gmail.com>
> <mailto:akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>>> wrote:
>
> On Wed, Aug 6, 2014 at 4:40 PM, Hadi <dinpajooh_at_gmail.com
> <mailto:dinpajooh_at_gmail.com>
> <mailto:dinpajooh_at_gmail.com <mailto:dinpajooh_at_gmail.com>>> wrote:
> > Axel,
> > This discussion is in NAMD list and it is about rigid
> models which
> use bond
> > 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.
>
> axel.
>
>
>
> > Thanks,
> > Hadi
> >
> >
> >
> > On Wed, Aug 6, 2014 at 1:28 PM, Axel Kohlmeyer
> <akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
> <mailto:akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>>> wrote:
> >>
> >> On Wed, Aug 6, 2014 at 3:41 PM, Hadi <dinpajooh_at_gmail.com
> <mailto:dinpajooh_at_gmail.com>
> <mailto:dinpajooh_at_gmail.com <mailto:dinpajooh_at_gmail.com>>> wrote:
> >> > In Monte Carlo, you do not need to use a constraint
> solver to
> implement
> >> > 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
> little
> >> > 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
> <mailto:akohlmey_at_gmail.com> <mailto:akohlmey_at_gmail.com
> <mailto: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
> <mailto:akohlmey_at_gmail.com> <mailto:akohlmey_at_gmail.com
> <mailto: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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