From: Basak Isin (isinbasak_at_yahoo.com)
Date: Mon Oct 11 2010 - 18:11:14 CDT
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
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
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>;
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
"Understanding Molecular Simulation" by Frenkel & Smit:
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
On Mon, 11 Oct 2010, Basak Isin wrote:
> 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
> solve the problems. It also gives to the other subscribes the idea that the
> was answered and they don't feel it is necessary to read the email or the
> 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
> before they turn to others but
> "Go and look at the literature." "Ask someone who is around you." "This
> 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
> If one has time and patience to reply to an email in a forum, she/he might also
> time to give the links that explains the basics, too.
> 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.
> > 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
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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