[gmx-users] PBS script

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 13 04:33:57 CEST 2010

manoj singh wrote:
> Hi Chris,
> Sorry if I have been rude is my response.
> I am new to the Gromacs-4.0. I just thought if some one can not give 
> positive response to the query, that person should not be responding as 
> this prohibits the further response to the topic.

There are no such rules here.  Everyone is welcome to comment if they have 
insight or tips.  My response was also not what I would call "not positive," 
rather an effort to genuinely help point you in the right direction.  In return, 
I received an insult.  In general, no one on this list will spoon-feed someone a 
procedure (especially when it seems that the individual has not done their 
homework) as it simply requires too much time for a simple mailing list.

Let's turn this situation into a learning experience.

Your first post suggested that you knew nothing about PBS or how to use Gromacs. 
  Based on your later posts, this is obviously not the case.  To get an 
effective response, you should do the following:

1. Post the script you're trying to use.
2. Post error message you're getting (if any), or otherwise describe (or better 
yet, cut-and-paste) relevant output from your queuing software that indicates 
the problem.
3. Understand that if someone suggests and additional resource, don't take it as 
dismissive.  You may simply be asking the wrong question, or perhaps asking the 
right question in the wrong place.  If I simply post the PBS script for use with 
my cluster, then some unsuspecting user will probably later on stumble across 
that post, take it out of context, and then blindly assume that it is the only 
correct way to use Gromacs, and we perpetuate a cycle of confusion.

For a few more tips:



> Again, thanks for your mail and sorry for my any irresponsible post.
> Manoj
> On Sun, Sep 12, 2010 at 6:25 PM, <chris.neale at utoronto.ca 
> <mailto:chris.neale at utoronto.ca>> wrote:
>     Manoj,
>     to suggest that Justin is being lazy would be to ignore the
>     hundreds, possibly thousands, of helpful posts that he has made on
>     the gromacs mailing list to assist users like yourself free of charge.
>     In fact, Justin was probably helping you more than you have realized
>     by pointing out that you can access some of this information in
>     places other than the gromacs mailing list, and yes, google is one
>     of those places.
>     Chris.
>     -- original message --
>     Thanks for reminding me the existence of Google.
>     It must be hard to copy and paste few lines of the PBS script than
>     advertising the Google.
>     On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul <jalemkul at
>     vt.edu <http://vt.edu>> wrote:
>         manoj singh wrote:
>             Thanks for the reply!
>             I will be very thankful if you can send me whatever you have.
>             I will change that according to my system.
>         If you know enough to make changes, then you probably know
>         enough to get up
>         and running.  A Google search for "example PBS script" turns up
>         nearly 4
>         million results, the first of which contains much of the
>         necessary basic
>         information.
>         -Justin
>     -- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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