>> Hi all, >> >> >> In the manual 3.3, given the formula (4.99), the formula (4.100) is wrong. >> There is the same mistake for formula (4.102). >> V has the form f * g² , so V' should be f'g² + 2fgg', whereas I read >> f'(g²+g'g). (Well, not exactly, there is also a parsing and a sign error). >> >> >> Had this mistake been done in the code too ?
>are you referring to table potentials? The equations you mention have neither f nor g I meant that the way to derive 4.100 (page 67) from 4.99 (page 66) is wrong. This is not the correct way to calculate the derivative of Vb. f and g are generic names for a function. Here, f = (1-lambda)ka + lambda*kb g = (b -(1-lambda)bA -lambda*bB) Berk replied that the code was correct anyway. -------- Message d'origine-------- De: [EMAIL PROTECTED] de la part de [EMAIL PROTECTED] Date: lun. 21/01/2008 15:46 À: [email protected] Objet : gmx-users Digest, Vol 45, Issue 86 Send gmx-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: source code change (Maik Goette) 2. t-coupling and freeze groups (Zhou Bo) 3. RE: Serious mistake in the manual ! In the code too ?! (Berk Hess) 4. Re: Serious mistake in the manual ! In the code too ?! (David van der Spoel) 5. Specified frame doesn't exist or file not seekable (Arnau Cordomi) 6. Re: Specified frame doesn't exist or file not seekable (Alan Dodd) 7. Re: Question Regarding Ligand-Enzyme Complex (Mark Zottola) 8. Re: Specified frame doesn't exist or file not seekable (Arnau Cordomi) ---------------------------------------------------------------------- Message: 1 Date: Mon, 21 Jan 2008 12:04:35 +0100 From: Maik Goette <[EMAIL PROTECTED]> Subject: Re: [gmx-users] source code change To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed You're welcome... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ avinash kumar wrote: > To Maik Goette, > > Thank you for your reply. > > Avinash Kumar > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > > . > ------------------------------ Message: 2 Date: Mon, 21 Jan 2008 20:27:02 +0800 From: "Zhou Bo" <[EMAIL PROTECTED]> Subject: [gmx-users] t-coupling and freeze groups To: <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" Hi gmx-users, I have a small question about the temperature set of the freeze groups. Does it make sense to set it to 0K for freeze groups, if not, how does it influence on the rest of systems? Thanks in advance. ------------------------------ Message: 3 Date: Mon, 21 Jan 2008 13:47:10 +0100 From: Berk Hess <[EMAIL PROTECTED]> Subject: [gmx-users] RE: Serious mistake in the manual ! In the code too ?! To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" ---------------------------------------- > Date: Mon, 21 Jan 2008 11:21:27 +0100 > From: [EMAIL PROTECTED] > To: [email protected] > Subject: Serious mistake in the manual ! In the code too ?! > > > Hi all, > > > In the manual 3.3, given the formula (4.99), the formula (4.100) is wrong. > There is the same mistake for formula (4.102). > V has the form f * g² , so V' should be f'g² + 2fgg', whereas I read > f'(g²+g'g). (Well, not exactly, there is also a parsing and a sign error). > > > Had this mistake been done in the code too ? No, the code is correct. Berk. _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ------------------------------ Message: 4 Date: Mon, 21 Jan 2008 14:06:27 +0100 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Serious mistake in the manual ! In the code too ?! To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed BON Michael wrote: > Hi all, > > > In the manual 3.3, given the formula (4.99), the formula (4.100) is wrong. > There is the same mistake for formula (4.102). > V has the form f * g² , so V' should be f'g² + 2fgg', whereas I read > f'(g²+g'g). (Well, not exactly, there is also a parsing and a sign error). > > > Had this mistake been done in the code too ? > are you referring to table potentials? The equations you mention have neither f nor g > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ------------------------------ Message: 5 Date: Mon, 21 Jan 2008 15:12:17 +0100 From: "Arnau Cordomi" <[EMAIL PROTECTED]> Subject: [gmx-users] Specified frame doesn't exist or file not seekable To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Dear all, I'm getting the following fatal error every time I try to use trjconv or any analysis program with "-b" flag on my .xtr files: Program trjconv, VERSION 3.3.2 Source code file: trxio.c, line: 635 Fatal error: Specified frame doesn't exist or file not seekable I executed gmxcheck and all files seem ok. Without the "-b" flag everything works perfectly. Is this a bug? I found that the same issue was reported a few months ago for version 3.3.1: http://www.gromacs.org/pipermail/gmx-users/2007-November/030484.html Thanks in advance, Arnau ------------------------------ Message: 6 Date: Mon, 21 Jan 2008 06:23:50 -0800 (PST) From: Alan Dodd <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Specified frame doesn't exist or file not seekable To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=us-ascii Check the bugzilla server, is it the same problem as #126? ----- Original Message ---- From: Arnau Cordomi <[EMAIL PROTECTED]> To: [email protected] Sent: Monday, January 21, 2008 2:12:17 PM Subject: [gmx-users] Specified frame doesn't exist or file not seekable Dear all, I'm getting the following fatal error every time I try to use trjconv or any analysis program with "-b" flag on my .xtr files: Program trjconv, VERSION 3.3.2 Source code file: trxio.c, line: 635 Fatal error: Specified frame doesn't exist or file not seekable I executed gmxcheck and all files seem ok. Without the "-b" flag everything works perfectly. Is this a bug? I found that the same issue was reported a few months ago for version 3.3.1: http://www.gromacs.org/pipermail/gmx-users/2007-November/030484.html Thanks in advance, Arnau _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ------------------------------ Message: 7 Date: Mon, 21 Jan 2008 09:30:20 -0500 From: "Mark Zottola" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Question Regarding Ligand-Enzyme Complex To: "Discussion list for GROMACS users" <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" I am following the tutorial given in the gromacs manual. While it does have a stepwise directions, there is a paucity of detail. The Dundee server is part of those directions. You are right, charge derivation is part of forcefield development. But which forcefield does this server use? And unless the forcefield is a fully united atom forcefield, the highly positive charge on nitrogen makes no sense. And if it is a united atom forcefield - why add hydrogens? If the forcefield includes only polar hydrogens, why do amino protons on a protonated NH2 group have a negative charge? These issues are above and beyond a simple read of wth Wiki on gromacs. So I again ask what is going on RE: my previous post. Mark > > > > All of the above is predicated on your choice of "force field" as a > model of physics. That server you mention produces topologies in a > manner (apparently - I know nothing about it) consistent with one such > force field. The primary source of information about it is the > publication in which they announced it. You should read about how it was > developed, and what method that server uses, and form your own > conclusions. Also, see here > http://wiki.gromacs.org/index.php/Parameterization > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080121/8068f9dd/attachment-0001.html ------------------------------ Message: 8 Date: Mon, 21 Jan 2008 15:46:02 +0100 From: "Arnau Cordomi" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Specified frame doesn't exist or file not seekable To: "Discussion list for GROMACS users" <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Hi Alan, It is indeed the same problem. Thanks a lot! Arnau 2008/1/21, Alan Dodd <[EMAIL PROTECTED]>: > Check the bugzilla server, is it the same problem as #126? > > > ----- Original Message ---- > From: Arnau Cordomi <[EMAIL PROTECTED]> > To: [email protected] > Sent: Monday, January 21, 2008 2:12:17 PM > Subject: [gmx-users] Specified frame doesn't exist or file not seekable > > Dear all, > > I'm getting the following fatal error every time I try to use trjconv > or any analysis program with "-b" flag on my .xtr files: > > Program trjconv, VERSION 3.3.2 > Source code file: trxio.c, line: 635 > > Fatal error: > Specified frame doesn't exist or file not seekable > > I executed gmxcheck and all files seem ok. Without the "-b" flag > everything works perfectly. Is this a bug? I found that the same issue > was reported a few months ago for version 3.3.1: > http://www.gromacs.org/pipermail/gmx-users/2007-November/030484.html > > Thanks in advance, > > Arnau > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > > > > ____________________________________________________________________________________ > Never miss a thing. Make Yahoo your home page. > http://www.yahoo.com/r/hs > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > ------------------------------ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 45, Issue 86 *****************************************
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