From: yi jiang (jy.namd_at_gmail.com)
Date: Mon Oct 11 2010 - 20:42:05 CDT
Hi,
Thank you guys for your kind help.
I read all the emails replying my question and I am so sorry that there
happened a little unpleasant arguments. I admit the question is so simple
and I understand that I should get more basic knowledge and search the
answer of those questions by myself before. That is more active and
effective.
Anyway, I know that it is for my own good that people replied my email.
Thank you guys very much for your attention and links. I am very
appreciated.
Best,
Yi Jiang
On Mon, Oct 11, 2010 at 6:54 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> if you are collecting recommendations for MD beginners,
> why not start a page on the NAMDWiki for that purpose?
>
> http://www.ks.uiuc.edu/Research/namd/wiki/
>
> that would make your efforts more permanent.
>
> axel.
>
> On Mon, Oct 11, 2010 at 7:11 PM, Basak Isin <isinbasak_at_yahoo.com> wrote:
> > 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.
> > -----------------------------------------------------
> >
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
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