[gmx-users] RE : Serious mistake in the manual !
BON Michael
michael.bon at cea.fr
Mon Jan 21 16:31:39 CET 2008
>> 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: gmx-users-bounces at gromacs.org de la part de gmx-users-request at gromacs.org
Date: lun. 21/01/2008 15:46
À: gmx-users at gromacs.org
Objet : gmx-users Digest, Vol 45, Issue 86
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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 <mgoette at mpi-bpc.mpg.de>
Subject: Re: [gmx-users] source code change
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <47947C43.3010408 at mpi-bpc.mpg.de>
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
> _______________________________________________
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> Please search the archive at http://www.gromacs.org/search before posting!
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> .
>
------------------------------
Message: 2
Date: Mon, 21 Jan 2008 20:27:02 +0800
From: "Zhou Bo" <zhoubo81 at gmail.com>
Subject: [gmx-users] t-coupling and freeze groups
To: <gmx-users at gromacs.org>
Message-ID: <001901c85c28$f2157980$d6406c80$@com>
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 <gmx3 at hotmail.com>
Subject: [gmx-users] RE: Serious mistake in the manual ! In the code
too ?!
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <BLU134-W689DB683E2F579A4B70298E3D0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------
> Date: Mon, 21 Jan 2008 11:21:27 +0100
> From: michael.bon at cea.fr
> To: gmx-users at gromacs.org
> 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.
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------------------------------
Message: 4
Date: Mon, 21 Jan 2008 14:06:27 +0100
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Serious mistake in the manual ! In the code
too ?!
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <479498D3.3010807 at xray.bmc.uu.se>
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 gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
------------------------------
Message: 5
Date: Mon, 21 Jan 2008 15:12:17 +0100
From: "Arnau Cordomi" <arnau.cordomi at gmail.com>
Subject: [gmx-users] Specified frame doesn't exist or file not
seekable
To: gmx-users at gromacs.org
Message-ID:
<3e388e410801210612w6d6e0916la326172388b4375d at mail.gmail.com>
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 <anoddlad at yahoo.com>
Subject: Re: [gmx-users] Specified frame doesn't exist or file not
seekable
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <104245.82896.qm at web38706.mail.mud.yahoo.com>
Content-Type: text/plain; charset=us-ascii
Check the bugzilla server, is it the same problem as #126?
----- Original Message ----
From: Arnau Cordomi <arnau.cordomi at gmail.com>
To: gmx-users at gromacs.org
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
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------------------------------
Message: 7
Date: Mon, 21 Jan 2008 09:30:20 -0500
From: "Mark Zottola" <mzottola at gmail.com>
Subject: Re: [gmx-users] Question Regarding Ligand-Enzyme Complex
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<cedbc7f30801210630s41b2c038wb3abca895d90a052 at mail.gmail.com>
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 gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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Message: 8
Date: Mon, 21 Jan 2008 15:46:02 +0100
From: "Arnau Cordomi" <arnau.cordomi at gmail.com>
Subject: Re: [gmx-users] Specified frame doesn't exist or file not
seekable
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<3e388e410801210646l4278e15cv7cfde36d3fc307f5 at mail.gmail.com>
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 <anoddlad at yahoo.com>:
> Check the bugzilla server, is it the same problem as #126?
>
>
> ----- Original Message ----
> From: Arnau Cordomi <arnau.cordomi at gmail.com>
> To: gmx-users at gromacs.org
> 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 gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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 gmx-users at gromacs.org
> 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
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