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

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 11 2010 - 18:54:28 CDT

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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