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

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Oct 13 2010 - 09:46:57 CDT

And it is done:

http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?BooksOnMolecularDynamics

The wiki limits the number of external links per page to discourage
spammers, but that shouldn't be a problem for a while. If anyone wants to
add comments on what books are good for what please do so.

-Jim

On Mon, 11 Oct 2010, Axel Kohlmeyer 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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