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" <[EMAIL PROTECTED]> >> Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> To: "Discussion list for GROMACS users" <gmx-users@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 <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED] >>> 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@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 [EMAIL PROTECTED] >> 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@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 [EMAIL PROTECTED] > 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 [EMAIL PROTECTED] o vai sul sito www.5xmille.org _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php