Re: Kb, Ktheta values for TIP3P water model

From: Hadi (dinpajooh_at_gmail.com)
Date: Wed Aug 06 2014 - 17:39:50 CDT

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> 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>> wrote:
>>
>> On Wed, Aug 6, 2014 at 4:40 PM, Hadi <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>> wrote:
>> >>
>> >> On Wed, Aug 6, 2014 at 3:41 PM, Hadi <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>
>>
>> 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>
>>
>> http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA,
>> USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>>
>>
>

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