Re: Kb, Ktheta values for TIP3P water model

From: Hadi (dinpajooh_at_gmail.com)
Date: Thu Aug 07 2014 - 12:36:33 CDT

Kenno,

I am happy you are directing the discussion to the right one, i.e., helping
others.

Let's focus on a rigid model in NAMD which uses bond constraint algorithm
(related to the original question) and neglect the comments that Alex
pointed out. He misunderstood my points and wanted to make me do an
inappropriate action.

Again, let's focus on a rigid model in NAMD which uses bond constraint
algorithm to incorporate the rigid bodies. This can be done by setting
rigidBonds to "all" in namd script.

Now if one uses a force constant value of 0 in the parameter file:
HT HT 0.00000 1.5139 ! ALLOW WAT
OT HT 0.000 0.9572 ! ALLOW WAT
The simulations become unstable.

Viswanath (the person who started the thread) was wondering what one should
do in this case. So I suggested to use reasonable force constants. One can
find them in the parameter file PARAM19

* - parameter file PARAM19 -
* PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
* TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
* JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1

Again, let me emphasize that the simulations become unstable, etc. if one
does not use reasonable force constants. It does not matter whether one
uses SHAKE or SETTLE algorithms.

Hope this helps.
Hadi

On Thu, Aug 7, 2014 at 8:50 AM, Kenno Vanommeslaeghe <
kvanomme_at_rx.umaryland.edu> wrote:

> 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.
>>
>>
>>
>>
>>
>

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:05 CST