Re: Simulating air with NAMD

From: Richard Wood (
Date: Mon May 07 2007 - 07:26:09 CDT

Dear Jim and others,

There is a reason for me to do object "in public" as I did. Mr. Abraham responds like this ALL the TIME, giving answers that are of absolutely no help to ANYONE, even to those of us that are more experienced; he obviously has never been a teacher. So, why does he bother to respond at all? He might as well just say, "go look it up in your textbook", when the person asking the question has no idea what to look up.

When I was working on my Ph.D., my advisor taught us to not "reinvent the wheel", and that is something I agree with. If Mr. Abraham and his ilk were in charge, we'd yet to have cars...

Richard L. Wood, Ph. D.

----- Original Message ----
From: Jim Phillips <>
To: Mark Abraham <>; Richard Wood <>
Cc: NAMD Users List <>
Sent: Sunday, May 6, 2007 11:31:27 PM
Subject: Re: namd-l: Simulating air with NAMD

Hi all,

I've generally been quite impressed with the level of discourse on NAMD-L,
so can we please restrict the bickering to private email? This particular
public exchange isn't making anyone look good.

First, the question is completely vague and asks how to do something
without any indication of the goal of the simulation. I assume that
Javier is young and inexperienced and has now learned better.

Second, Mark's response contains no more information than RTFM and STFW
(see for definitions).
If he felt compelled to respond publicly, it would have been better to
point out the vagueness of the question and ask for clarification.

Third, Richard points out the uselessness of Mark's response. There was
no reason to do this in public. Mark naturally takes offense, in public.

Fortunately, the rest of NAMD-L has been mature enough to let it pass and
get back to discussing science. Miraculously, Jeff Potoff has now popped
up with genuine expertise on gas-phase simulations, which is the kind of
response people are hoping for when they ask questions. Thanks, Jeff!


On Mon, 7 May 2007, Mark Abraham wrote:

> Richard Wood wrote:
>> I.e., why bother responding if you're going to be like this?
> Richard, I'm getting sick of this harassment. I answered the question
> pointing out some pertinent steps they need either to do themselves or to
> find out whether someone else has done them and copy/borrow. I didn't do any
> of their work for them, which seems to be your regular grievance with me. I'm
> one of the most frequent contributors to the GROMACS list, and not once has
> anybody objected to the way I answer questions there. I have better things to
> do than give free help on this list, and much better things to do than listen
> to you complain non-constructively when I do. If what I'm doing is so wrong,
> then please teach me what I should be doing, please explain why I should be
> doing it, and please explain why nobody else is objecting.
> Mark
>> > How could I find a way to simulate air with NAMD?. I mean pdb, psf and
>> > prm files.
>> It's possible, you just need to find a parameter set for gas-phase
>> simulations (i.e. search the literature) which may need to be converted
>> to a suitable format (i.e. read the documentation), and generate a
>> starting structure and topology as you would for a condensed-phase
>> simulation.
>> Mark

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