[gmx-users] peptide coming out of the box

[Berk Hess]

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
> >>>
> >>>
> >>> _______________________________________________
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> >>>
> >>
> >>
> >> --
> >> 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
> >> _______________________________________________
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> >
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>
>--
>-------------------------------
>Andrea Spitaleri PhD
>Dulbecco Telethon Institute
>c/o DIBIT Scientific Institute
>Biomolecular NMR, 1B4
>Via Olgettina 58
>20132 Milano (Italy)
>http://biomolecularnmr.ihsr.dom/
>-------------------------------
>
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