From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 11 2010 - 15:16:21 CDT
On Mon, Oct 11, 2010 at 3:56 PM, Basak Isin <isinbasak_at_yahoo.com> 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
> 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
> 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.
it is meant to discourage people to ask questions without
spending some effort on their own. it has become common
practice to rather spew out a few random questions (ideally
cross-posted to many mailing lists) before even thinking about
what the answer would be.
there is a very important relation between a question and its answer:
the answer can on average only be as good as the question.
thus if you want to see a "better" answer, you may have to ask
a "better" question.
> 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.
an important part of learning is to find the right forum
to ask the right question.
this is not a forum to ask questions about elementary MD issues.
it is about the NAMD simulation program. one has to assume that
a person asking questions show that he/she has at least spent
some effort to "make his/her home work".
while it may sound rude to not answer a question and send
somebody elsewhere, i am convinced - from lots of personal
experience i might add - that this is the by far best way to get
the kind of help the original poster is looking for. behind this
simple question are looming many details (and more questions)
that also need to be answered and that is effectively impossible
to do via e-mail. i have been there. with some minimal effort on
a search engine, however, lots of useful resources can be found,
even by a beginner, but then it is _essential_ to find a local expert
to discuss (or take classes, participate in proper tutorials, and so on).
other than that. i can only encourage you to prove me wrong
and answer the questions asked and see where this leads.
> 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
>> what I understand, it seems that people just need one of the two methods
>> 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
> 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.
-- 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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