Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial

From: Basak Isin (isinbasak_at_yahoo.com)
Date: Mon Oct 11 2010 - 18:11:14 CDT

Hi,
I was not the person who asked the question in the first place so I am ccing
your email to the person (Yi Jiang) who sent the email with the questions about
PME

and Langevian dynamics.

Thanks for the link. I also used Frenkel & Smit a lot during my PHD as well as
my officemate. :o)

I also like this one below. I think it is great for beginners but it is super
expensive. I used to get it from the library.

Computational Biochemistry and Biophysics
Oren M. Becker, Alexander D. MacKerell Jr., Benoit Roux , Masakatsu Watanabe
http://www.amazon.com/Computational-Biochemistry-Biophysics-Oren-Becker/dp/082470455X

Thanks!!!
Basak

 Basak Isin

ABOVE ALL NATIONS IS HUMANITY.
"What matters - all that matters, really - is the will to happiness, a kind of
enormous, ever-present consciousness. The rest - women, art, success - is
nothing but excuses." - Albert Camus

Cause life is meant for living. Yaki-da ;o)

________________________________
From: Gianluca Interlandi <gianluca_at_u.washington.edu>
To: Basak Isin <isinbasak_at_yahoo.com>
Cc: Axel Kohlmeyer <akohlmey_at_gmail.com>; yi jiang <jy.namd_at_gmail.com>;
namd-l_at_ks.uiuc.edu
Sent: Mon, October 11, 2010 5:56:03 PM
Subject: Re: Regarding answering questions in a forum. Re: namd-l: Langevin
process in NAMD tutorial

Good reference:

"Understanding Molecular Simulation" by Frenkel & Smit:

http://www.amazon.com/Understanding-Molecular-Simulation-Second-Computational/dp/0122673514

There, you will find a nice description of Particle Mesh Ewald (PME) and
thermostats like Langevin. This is the book anybody who does MD should have in
his shelf.

Gianluca

On Mon, 11 Oct 2010, Basak Isin wrote:

> Hi,
> I really felt the need to respond to this email.
>
> >>Which one is actually used in the example? Or they are used to deal with
> >> different problems?
>
> >both. they PME and Langevin serve different purposes.
>
> When these kinds of answers are given to the questions, they do not help so
>much to
> solve the problems. It also gives to the other subscribes the idea that the
>question
> was answered and they don't feel it is necessary to read the email or the
>question
> since they start thinking that it was already answered.
>
> I agree that people have to learn and do as much as possible to solve their
>problems
> before they turn to others but
>
> "Go and look at the literature." "Ask someone who is around you." "This
>question
> shows that you and your system admin do not really know this or anything...."
> answers do not really help anybody. It may also discourage people from asking
> questions.
>
> If one has time and patience to reply to an email in a forum, she/he might also
>
>have
> time to give the links that explains the basics, too.
>
> Thanks
> Basak
>
>
>_____________________________________________________________________________________
>
>_
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: yi jiang <jy.namd_at_gmail.com>
> Cc: namd-l_at_ks.uiuc.edu
> Sent: Mon, October 11, 2010 1:21:04 PM
> Subject: Re: namd-l: Langevin process in NAMD tutorial
>
> On Mon, Oct 11, 2010 at 12:14 PM, yi jiang <jy.namd_at_gmail.com> wrote:
> > Dear all,
> >
> > I am a new to NAMD and have a basic question about the Langevin process in
> > NAMD tutorial.
> >
> > I noticed in example 3 (1-3-box), both PME and Langevin process are
> > activated in the configuration file "ubq_wb_eq.conf". However, according to
> > what I understand, it seems that people just need one of the two methods to
> > do MD.
> >
> > Which one is actually used in the example? Or they are used to deal with
> > different problems?
>
> both. they PME and Langevin serve different purposes.
>
> > I will be very appreciated if there is someone answer this basic question
> > explicitly.
>
> please understand, that this is not the right forum to discuss such
> fundamental matters. get hold of a text book on molecular dynamics
> and look it up. ...and then find somebody locally to discuss topics
> related to MD. these kind of questions are so much better answered,
> if you would spend some effort in figuring them out by yourself and
> then discuss your findings with somebody more knowledgable in
> a dialogue.
>
> cheers,
> axel.
>
>
> >
> > Thank you for your attention.
> >
> > Yi Jiang
> >
> > --------------------------------
> > Graduate student
> > Department of Mathematical Sciences
> > University of Wisconsin Milwaukee
> > Milwaukee, WI 53211
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

      

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