[gmx-users] peptide coming out of the box

Tue Mar 20 13:03:25 CET 2007

Maybe we can add a filter, which automatically deflects mails with
certain key words, possibly giving a link to the FAQ :)

But seriously, I think this would be a good point to add to the FAQ.
Also, adding a "dummy" user list isn't an option. It is annoying
anyway to get the exact same question(s) once or more every week,
which is exactly what is happening with peptide/protein/molecule jumps
out of the solvent...

It may also be a good idea to spend some words (and examples) on these
matters in the tutorials. Thinking of it, a "dummy" manual might be a
good idea (including a section how to deal with dummies on user
lists), but I would hope that people would read some general texts
about molecular simulations before they embark on it.

Tsjerk

On 3/20/07, Berk Hess <gmx3 at hotmail.com> wrote:
>
> I think one user mailing list is enough, otherwise people will not
> know where to post their questions. Now we already get some
> user questions on the developers list.
>
> My point was more that people should first search and the ask.
> But probably never 100% of the users will do this.
>
> Another idea might be to have a link to the faq on the mailing
> list pages, with the suggestion to read that before posting.
> And we should add protein/peptide/molecule out of the box
> to the faq, since it doesn't seem to be there.
> That's a mistake on our side.
>
> Berk.
>
> >From: andrea spitaleri <spitaleri.andrea at hsr.it>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] peptide coming out of the box
> >Date: Tue, 20 Mar 2007 12:02:40 +0100
> >
> >Hi,
> >why do not think about a beginners mailing list or gromacs for dummies?
> >of course this is my humble opinion to you guys ....
> >and of course  I agree with you in searching **always before** in the list
> >archive ..
> >This is just a suggestion ...
> >
> >Regards,
> >
> >andrea
> >
> >Berk Hess wrote:
> > > Maybe we should let people do a test before they can become member
> > > of the mailing list. We already have two questions:
> > > Can you search the list archive?
> > > It is a problem when a peptide comes out of the box?
> > >
> > > Berk.
> > >
> > >> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> > >> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > >> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > >> Subject: Re: [gmx-users] peptide coming out of the box
> > >> Date: Tue, 20 Mar 2007 11:30:18 +0100
> > >>
> > >> Oh no.., not again!
> > >>
> > >> Read the manual, browse the archives and try to understand periodic
> > >> boundary conditions!
> > >> (and use trjconv -fit translate or trjconv -center on your trajectory)
> > >>
> > >> Tsjerk
> > >>
> > >> On 3/20/07, priya priya <priyaanand_27 at yahoo.co.in> wrote:
> > >>> Dear all
> > >>>
> > >>>  I started with 6 residue peptide simulation in water for 1ns.
> > >>> initially i
> > >>> placed the peptide in the center using the command editconf -c flag,
> >but
> > >>> after MD peptide is coming out of the water box. I want to calculate
> >the
> > >>> water molecules around it and peptide interactions with water.
> > >>>
> > >>>  Is there an error running simulation.
> > >>>  Regards
> > >>>  Priya
> > >>>
> > >>>
> > >>>  ________________________________
> > >>>  Here's a new way to find what you're looking for - Yahoo! Answers
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> gmx-users mailing list    gmx-users at gromacs.org
> > >>> http://www.gromacs.org/mailman/listinfo/gmx-users
> > >>> Please don't post (un)subscribe requests to the list. Use the
> > >>> www interface or send it to gmx-users-request at gromacs.org.
> > >>> Can't post? Read
> > >>> http://www.gromacs.org/mailing_lists/users.php
> > >>>
> > >>
> > >>
> > >> --
> > >> Tsjerk A. Wassenaar, Ph.D.
> > >> Junior UD (post-doc)
> > >> Biomolecular NMR, Bijvoet Center
> > >> Utrecht University
> > >> Padualaan 8
> > >> 3584 CH Utrecht
> > >> The Netherlands
> > >> P: +31-30-2539931
> > >> F: +31-30-2537623
> > >> _______________________________________________
> > >> gmx-users mailing list    gmx-users at gromacs.org
> > >> http://www.gromacs.org/mailman/listinfo/gmx-users
> > >> Please don't post (un)subscribe requests to the list. Use the www
> > >> interface or send it to gmx-users-request at gromacs.org.
> > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > > _________________________________________________________________
> > > Talk with your online friends with Messenger
> > > http://www.join.msn.com/messenger/overview
> > >
> > > _______________________________________________
> > > gmx-users mailing list    gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the www
> > > interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> >
> >--
> >-------------------------------
> >Andrea Spitaleri PhD
> >Dulbecco Telethon Institute
> >c/o DIBIT Scientific Institute
> >Biomolecular NMR, 1B4
> >Via Olgettina 58
> >20132 Milano (Italy)
> >http://biomolecularnmr.ihsr.dom/
> >-------------------------------
> >
> >********************************************************************
> >Sostieni la ricerca del San Raffaele con il 5permille!
> >E' SEMPLICE E NON COSTA NULLA.
> >Basta indicare nell'apposito riquadro della dichiarazione dei
> >redditi ("Ricerca sanitaria")
> >il codice fiscale della
> >Fondazione Centro S. Raffaele del Monte Tabor:
> >03 06 42 80 153 e ricordarsi di firmare.
> >Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai sul sito
> >www.5xmille.org
> >_______________________________________________
> >gmx-users mailing list    gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> _________________________________________________________________
> Live Search, for accurate results! http://www.live.nl
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623