[gmx-users] Re: gmx-users Digest, Vol 55, Issue 150

Q. Y. HUAN scottiehuan at yahoo.com
Sat Nov 29 11:53:59 CET 2008


Dear Justin and all,
 In my results, that are not only 8 micelles but there are 2 aggregated micelles and some free monomers that made up total of 8.
Then the graph also showed 8 number of clusters. that is what I am wonder is it monomer also counted?
thanks for any comments.

QIU YI HUAN
A beginner of Gromacs user.


--- On Fri, 11/28/08, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org> wrote:

> From: gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
> Subject: gmx-users Digest, Vol 55, Issue 150
> To: gmx-users at gromacs.org
> Date: Friday, November 28, 2008, 11:21 PM
> Send gmx-users mailing list submissions to
> 	gmx-users at gromacs.org
> 
> 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
> 	gmx-users-request at gromacs.org
> 
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> 	gmx-users-owner at gromacs.org
> 
> When replying, please edit your Subject line so it is more
> specific
> than "Re: Contents of gmx-users digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: Analyzing a trajectory split over multiple files
> (TJ Piggot)
>    2. Re: Fatal error with grompp(with detail process)
>       (Justin A. Lemkul)
>    3. Re: Re: Re: defination of cluster (Justin A. Lemkul)
>    4. RE: Box vector shifts number in x and y/z dimension
> (Berk Hess)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 28 Nov 2008 11:47:55 +0000
> From: TJ Piggot <t.piggot at bristol.ac.uk>
> Subject: Re: [gmx-users] Analyzing a trajectory split over
> multiple
> 	files
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <D53A8A4D4CC92A0039EF10AA at bch-oracle.bch.bris.ac.uk>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed
> 
> Just as a note most analysis tools have a -noxvgr option to
> output the 
> results without any of the formatting information for
> grace.
> 
> Also I still think the easiest way to solve your problem is
> to just 
> initially use trjcat to concatenate your trajectory, then
> run the analysis 
> on this.
> 
> Tom
> 
> --On Friday, November 28, 2008 05:06:31 +0530 Suman
> Chakrabarty 
> <suman at sscu.iisc.ernet.in> wrote:
> 
> > On Fri, Nov 28, 2008 at 4:24 AM, Nicolas
> <nsapay at ucalgary.ca> wrote:
> >> Suman Chakrabarty a écrit :
> >>> It would have been much easier if there was
> some way to concatenate
> >>> the multiple .xvg files easily. Also, the
> analysis programs should be
> >>> able to export the output data in raw 2 (or
> more) column format
> >>> without all the formatting statements as an
> option.
> >>>
> >>
> >> Actually, there is:
> >>
> >> grep -v "^#" *.xvg > concatenate.xvg
> >>
> >> The -v "^#" will skip all the comment
> lines of your xvg files. Of course,
> >> this assumes that your xvg files are correctly
> named, i.e. file01.xvg,
> >> file02.xvg, etc. With a short shell script, you
> can easily re-add the
> >> comments at the beginning of your concatenate
> file, renumber the frames
> >> correctly, etc. It is more convenient to write a
> Python or a Perl script
> >> to do this kind of stuff, though.
> >>
> >> Nicolas
> >
> >
> >
> > Thank you very much! I always knew there must be
> something smart to be
> > done. I should now delve into the nitty-gritty of
> scripting. grep
> > seems to be a particularly useful tool! :)
> >
> >
> > Regards,
> > Suman.
> 
> 
> 
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 28 Nov 2008 07:25:28 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Fatal error with grompp(with
> detail process)
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <492FE338.2020904 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> Jenny Hsu wrote:
> > Hi all:
> > I have a problem with grompp
> > I want to making "POPC+protein" file
> > and I search the archieve and follow the process
> > 1.run pdb2gmx for protein only
> > 2.add below parameters into my topology file
> >  #include "ffG53a6.itp"
> >  #include "lipid.itp"
> >  #include "popc.itp"
> > 3.adjust the [ molecules ] section to list the number
> and type of my 
> > components  
> > 4.run editconf and genbox
> > 5.run grompp and it shows
> > Fatal error:
> > Atomtype CA not found
> 
> We just had a discussion about this:
> 
> http://www.gromacs.org/pipermail/gmx-users/2008-November/038282.html
> 
> You can copy the relevant portions of lipid.itp into the
> appropriate sections in 
> ffG53a6nb.itp/ffG53a6bon.itp.  Otherwise, including the
> files as you have will 
> not work.
> 
> -Justin
> 
> >  
> > *Below is all information it shows*
> > *Can someone help me to solve this problem?*
> > *I am appreciate with that.*
> > *Thaks.*
> >         :-)  G  R  O  M  A  C  S  (-:
> >         Getting the Right Output Means no Artefacts in
> Calculating Stuff
> >                              :-)  VERSION 4.0  (-:
> >       Written by David van der Spoel, Erik Lindahl,
> Berk Hess, and others.
> >        Copyright (c) 1991-2000, University of
> Groningen, The Netherlands.
> >              Copyright (c) 2001-2008, The GROMACS
> development team,
> >             check out http://www.gromacs.org
> <http://www.gromacs.org/> 
> > for more information.
> >          This program is free software; you can
> redistribute it and/or
> >           modify it under the terms of the GNU General
> Public License
> >          as published by the Free Software Foundation;
> either version 2
> >              of the License, or (at your option) any
> later version.
> >                                 :-)  grompp  (-:
> > Option     Filename  Type         Description
> >
> ------------------------------------------------------------
> >   -f         em.mdp  Input, Opt!  grompp input file
> with MD parameters
> > -po      mdout.mdp  Output       grompp input file
> with MD parameters
> >   -c 1UEO-nowater_water.gro  Input        Structure
> file: gro g96 pdb 
> > tpr tpb
> >                                    tpa
> >   -r       conf.gro  Input, Opt.  Structure file: gro
> g96 pdb tpr tpb tpa
> > -rb       conf.gro  Input, Opt.  Structure file: gro
> g96 pdb tpr tpb tpa
> >   -n      index.ndx  Input, Opt.  Index file
> >   -p 1UEO-nowater.top  Input        Topology file
> > -pp  processed.top  Output, Opt. Topology file
> >   -o 1UEO-nowater_em.tpr  Output       Run input file:
> tpr tpb tpa
> >   -t       traj.trr  Input, Opt.  Full precision
> trajectory: trr trj cpt
> >   -e       ener.edr  Input, Opt.  Energy file: edr ene
> > Option       Type   Value   Description
> > ------------------------------------------------------
> > -[no]h       bool   no      Print help info and quit
> > -nice        int    0       Set the nicelevel
> > -[no]v       bool   yes     Be loud and noisy
> > -time        real   -1      Take frame at or first
> after this time.
> > -[no]rmvsbds bool   yes     Remove constant bonded
> interactions with virtual
> >                             sites
> > -maxwarn     int    0       Number of allowed warnings
> during input 
> > processing
> > -[no]zero    bool   no      Set parameters for bonded
> interactions without
> >                             defaults to zero instead
> of generating an error
> > -[no]renum   bool   yes     Renumber atomtypes and
> minimize number of
> >                             atomtypes
> > Ignoring obsolete mdp entry 'title'
> > Ignoring obsolete mdp entry 'cpp'
> > Back Off! I just backed up mdout.mdp to
> ./#mdout.mdp.2#
> > checking input for internal consistency...
> > processing topology...
> > Opening library file
> /usr/local/md/share/gromacs/top/ffG53a6.itp
> > Opening library file
> /usr/local/md/share/gromacs/top/ffG53a6nb.itp
> > Opening library file
> /usr/local/md/share/gromacs/top/ffG53a6bon.itp
> > Opening library file
> /usr/local/md/share/gromacs/top/ff_dum.itp
> > WARNING 1 [file lipid.itp, line 14]:
> >   Overriding atomtype LO
> > WARNING 2 [file lipid.itp, line 15]:
> >   Overriding atomtype LOM
> > WARNING 3 [file lipid.itp, line 16]:
> >   Overriding atomtype LNL
> > WARNING 4 [file lipid.itp, line 17]:
> >   Overriding atomtype LC
> > WARNING 5 [file lipid.itp, line 18]:
> >   Overriding atomtype LH1
> > WARNING 6 [file lipid.itp, line 19]:
> >   Overriding atomtype LH2
> > WARNING 7 [file lipid.itp, line 20]:
> >   Overriding atomtype LP
> > WARNING 8 [file lipid.itp, line 21]:
> >   Overriding atomtype LOS
> > WARNING 9 [file lipid.itp, line 22]:
> >   Overriding atomtype LP2
> > WARNING 10 [file lipid.itp, line 23]:
> >   Overriding atomtype LP3
> > WARNING 11 [file lipid.itp, line 24]:
> >   Overriding atomtype LC3
> > WARNING 12 [file lipid.itp, line 25]:
> >   Overriding atomtype LC2
> > WARNING 13 [file lipid.itp, line 108]:
> >   Overriding non-bonded parameters,
> >   old: 0.00238804 3.38411e-06 new
> > LNL     C   1   2.387718e-03 2.389594e-06
> >
> -------------------------------------------------------
> > Program grompp, VERSION 4.0
> > Source code file: toppush.c, line: 793
> > Fatal error:
> > Atomtype CA not found
> >  
> >  
> > -- 
> > Jenny Hsu, Biotechnology Dept.,
> > Ming Chuan University, Taiwan, R.O.C
> > 
> > 
> >
> ------------------------------------------------------------------------
> > 
> > _______________________________________________
> > 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
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Fri, 28 Nov 2008 07:29:12 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Re: defination of cluster
> To: scottiehuan at yahoo.com,	Discussion list for GROMACS
> users
> 	<gmx-users at gromacs.org>
> Message-ID: <492FE418.2040001 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> 
> 
> Q. Y. HUAN wrote:
> > Dear Mark and all,
> > Yes, I read it before I start. It states that the
> program computes the size distributions of molecular/atomic
> clusters in gas phase. Is it means   that even a single
> molecule, it is also defined as a cluster?
> > Thanks for the help.
> > 
> > 
> 
> In my mind, that would make no sense.  Also, think about
> your results that you 
> told us about - 8 micelles, and 8 aggregates detected.  Do
> you think that the 
> monomers are being considered?
> 
> -Justin
> 
> > 
> > 
> > QIU YI HUAN
> > DEPARTMENT OF CHEMISTRY,
> > FACULTY OF SCIENCE,
> > UNIVERSITY PUTRA MALAYSIA,
> > MALAYSIA.
> > 
> > 
> > --- On Fri, 11/28/08, gmx-users-request at gromacs.org
> <gmx-users-request at gromacs.org> wrote:
> > 
> >> From: gmx-users-request at gromacs.org
> <gmx-users-request at gromacs.org>
> >> Subject: gmx-users Digest, Vol 55, Issue 147
> >> To: gmx-users at gromacs.org
> >> Date: Friday, November 28, 2008, 3:59 PM
> >> Send gmx-users mailing list submissions to
> >> 	gmx-users at gromacs.org
> >>
> >> 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
> >> 	gmx-users-request at gromacs.org
> >>
> >> You can reach the person managing the list at
> >> 	gmx-users-owner at gromacs.org
> >>
> >> When replying, please edit your Subject line so it
> is more
> >> specific
> >> than "Re: Contents of gmx-users
> digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >>    1. Re: defination of cluster (Mark Abraham)
> >>    2. Box vector shifts number in x and y/z
> dimension
> >> (xuji)
> >>    3. How to calculate virial in gromacs-4.0?
> (xuji)
> >>    4. RE: PME-user for electrostatics (Berk Hess)
> >>    5. Fatal error with grompp(with detail process)
> (Jenny
> >> Hsu)
> >>
> >>
> >>
> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Fri, 28 Nov 2008 12:24:52 +1100
> >> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> >> Subject: Re: [gmx-users] defination of cluster
> >> To: Discussion list for GROMACS users
> >> <gmx-users at gromacs.org>
> >> Message-ID: <492F4864.9050402 at anu.edu.au>
> >> Content-Type: text/plain; charset=ISO-8859-1;
> format=flowed
> >>
> >> Q. Y. HUAN wrote:
> >>> Dear all, 
> >>>
> >>> I did the g_clustsize to get the number of
> cluster
> >> graph for my system. At the end of the simulation,
> the total
> >> number of cluster shown in the graph of my system
> was 8.
> >> Then I had a view in the trjectory and I found
> that there
> >> were total of 8 aggregated micelles and some free
> monomer
> >> (even it is a single molecule) which is same with
> the result
> >> shown in the graph.
> >>> ie 8 in the graph, 8 in the trajectory
> >>>
> >>>
> >>> My question is, how Gromacs define the
> defination of
> >> cluster? In my case, is it a free monomer (single
> free
> >> molecule) is also counted?
> >>
> >> Did you start by reading g_clustsize -h?
> >>
> >> Mark
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Fri, 28 Nov 2008 09:41:31 +0800
> >> From: "xuji"<xuji at home.ipe.ac.cn>
> >> Subject: [gmx-users] Box vector shifts number in x
> and y/z
> >> dimension
> >> To: "gmx-users at gromacs.org"
> >> <gmx-users at gromacs.org>
> >> Message-ID:
> >> <20081128014452.DB941197 at colibri.its.uu.se>
> >> Content-Type:
> text/plain;	charset="gb2312"
> >>
> >> Hi all:
> >>
> >> In gromacs all atoms are in the rectangular or
> triclinic
> >> unit-cell,
> >> and in the codes using shifts with periodic
> boundary
> >> condition.
> >> But why are there only single box vector shifts
> required in
> >> y and z dimensions 
> >> but 2 in x dimension ?
> >>
> >> Thanks for any help in advance!
> >> 				 
> >>
>         xuji
> >>
>         xuji at home.ipe.ac.cn
> >>
>           2008-11-28
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 3
> >> Date: Fri, 28 Nov 2008 15:32:55 +0800
> >> From: "xuji"<xuji at home.ipe.ac.cn>
> >> Subject: [gmx-users] How to calculate virial in
> >> gromacs-4.0?
> >> To: "gmx-users at gromacs.org"
> >> <gmx-users at gromacs.org>
> >> Message-ID:
> >> <20081128073315.3E84B233 at colibri.its.uu.se>
> >> Content-Type:
> text/plain;	charset="gb2312"
> >>
> >> Hi all
> >>
> >> I want to do pressure coupling in my own program.
> >> So These days I read associated codes in
> Gromacs_4.0 and I
> >> find that it
> >> must sum the virial first. In Gromacs-3.3.3 you
> use the
> >> intramolecular shift(graph)
> >> to sum the virial of the covalent bonds, but in
> Gromacs-4.0
> >> the graph variable seems to be NULL
> >> when run the mdrun with domain decomposition. Is
> it the
> >> true? 
> >> And if it's true how do you sum the virial
> with the
> >> periodic boundary condition 
> >> in Gromacs_4.0 with domain decomposition? Can
> someone
> >> explain the way of summing 
> >> virial in Gromacs_4.0 in detail? Or can you
> recommend some
> >> resoures about summing the virial with 
> >> the periodic boundary condition? 
> >> 	
> >> Appreciate any help in advance!
> >>
> >> Best
> >> 	wishes!
> >>  				
> >>
> >>
>         xuji
> >>
>         xuji at home.ipe.ac.cn
> >>
>           2008-11-28
> >>
> >> ------------------------------
> >>
> >> Message: 4
> >> Date: Fri, 28 Nov 2008 08:56:16 +0100
> >> From: Berk Hess <gmx3 at hotmail.com>
> >> Subject: RE: [gmx-users] PME-user for
> electrostatics
> >> To: Discussion list for GROMACS users
> >> <gmx-users at gromacs.org>
> >> Message-ID:
> >>
> <BLU134-W4572A3387EFBAA5982B92F8E040 at phx.gbl>
> >> Content-Type: text/plain;
> charset="iso-8859-1"
> >>
> >>
> >> Hi,
> >>
> >> PME splits the calculation in a Mesh part and a
> direct
> >> space part,
> >> which is normally 1/r minus the mesh part. Note
> that the
> >> mesh part
> >> also contributes below the cut-off.
> >> If you want something else than 1/r at short range
> >> (you always have 1/r beyond the cut-off)
> >> than you can just give the short-range potential
> you want,
> >> mdrun takes care that it subtracts the short range
> >> contribution of the mesh part.
> >>
> >> Berk
> >>
> >>> Date: Thu, 27 Nov 2008 13:37:36 -0800
> >>> From: argyriosk at yahoo.com
> >>> To: gmx-users at gromacs.org
> >>> Subject: [gmx-users] PME-user for
> electrostatics
> >>>
> >>> hi, 
> >>>
> >>> i want to use a different function than the
> Coulomb to
> >> calculate the electrostatics 
> >>> between charged ions. So i am thinking to user
> the
> >> PME-user option for the electrostatics.
> >>> The manual says for the PME-user
> option"The PME
> >> mesh contribution is subtracted from the user
> table by
> >> mdrun".
> >>> what that means?  should i have to add the
> >> short-range-potential (given by equation-4.33 in
> the manual)
> >>> in the user table, because that will be
> subtracted
> >> with the mdrun? 
> >>> please let me know,  and thanks a lot for your
> help
> >>>
> >>>
> >>>       
> >>>
> _______________________________________________
> >>> 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
> >>
> >>
> _________________________________________________________________
> >> Express yourself instantly with MSN Messenger!
> Download
> >> today it's FREE!
> >>
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> >> ------------------------------
> >>
> >> Message: 5
> >> Date: Fri, 28 Nov 2008 15:58:41 +0800
> >> From: "Jenny Hsu"
> <jenny.h1087 at gmail.com>
> >> Subject: [gmx-users] Fatal error with grompp(with
> detail
> >> process)
> >> To: "Discussion list for GROMACS users"
> >> <gmx-users at gromacs.org>
> >> Message-ID:
> >>
> 	<f2f16de70811272358s39ae1940ibff7ec6c7f20c2b at mail.gmail.com>
> >> Content-Type: text/plain;
> charset="iso-8859-1"
> >>
> >> Hi all:
> >> I have a problem with grompp
> >> I want to making "POPC+protein" file
> >> and I search the archieve and follow the process
> >> 1.run pdb2gmx for protein only
> >> 2.add below parameters into my topology file
> >>  #include "ffG53a6.itp"
> >>  #include "lipid.itp"
> >>  #include "popc.itp"
> >> 3.adjust the [ molecules ] section to list the
> number and
> >> type of my
> >> components
> >> 4.run editconf and genbox
> >> 5.run grompp and it shows
> >> Fatal error:
> >> Atomtype CA not found
> >>
> >> *Below is all information it shows*
> >> *Can someone help me to solve this problem?*
> >> *I am appreciate with that.*
> >> *Thaks.*
> >>         :-)  G  R  O  M  A  C  S  (-:
> >>         Getting the Right Output Means no
> Artefacts in
> >> Calculating Stuff
> >>                              :-)  VERSION 4.0  (-:
> >>       Written by David van der Spoel, Erik
> Lindahl, Berk
> >> Hess, and others.
> >>        Copyright (c) 1991-2000, University of
> Groningen,
> >> The Netherlands.
> >>              Copyright (c) 2001-2008, The GROMACS
> >> development team,
> >>             check out http://www.gromacs.org for
> more
> >> information.
> >>          This program is free software; you can
> >> redistribute it and/or
> >>           modify it under the terms of the GNU
> General
> >> Public License
> >>          as published by the Free Software
> Foundation;
> >> either version 2
> >>              of the License, or (at your option)
> any later
> >> version.
> >>                                 :-)  grompp  (-:
> >> Option     Filename  Type         Description
> >>
> ------------------------------------------------------------
> >>   -f         em.mdp  Input, Opt!  grompp input
> file with MD
> >> parameters
> >> -po      mdout.mdp  Output       grompp input file
> with MD
> >> parameters
> >>   -c 1UEO-nowater_water.gro  Input       
> Structure file:
> >> gro g96 pdb tpr
> >> tpb
> >>                                    tpa
> >>   -r       conf.gro  Input, Opt.  Structure file:
> gro g96
> >> pdb tpr tpb tpa
> >> -rb       conf.gro  Input, Opt.  Structure file:
> gro g96
> >> pdb tpr tpb tpa
> >>   -n      index.ndx  Input, Opt.  Index file
> >>   -p 1UEO-nowater.top  Input        Topology file
> >> -pp  processed.top  Output, Opt. Topology file
> >>   -o 1UEO-nowater_em.tpr  Output       Run input
> file: tpr
> >> tpb tpa
> >>   -t       traj.trr  Input, Opt.  Full precision
> >> trajectory: trr trj cpt
> >>   -e       ener.edr  Input, Opt.  Energy file: edr
> ene
> >> Option       Type   Value   Description
> >>
> ------------------------------------------------------
> >> -[no]h       bool   no      Print help info and
> quit
> >> -nice        int    0       Set the nicelevel
> >> -[no]v       bool   yes     Be loud and noisy
> >> -time        real   -1      Take frame at or first
> after
> >> this time.
> >> -[no]rmvsbds bool   yes     Remove constant bonded
> >> interactions with virtual
> >>                             sites
> >> -maxwarn     int    0       Number of allowed
> warnings
> >> during input
> >> processing
> >> -[no]zero    bool   no      Set parameters for
> bonded
> >> interactions without
> >>                             defaults to zero
> instead of
> >> generating an error
> >> -[no]renum   bool   yes     Renumber atomtypes and
> minimize
> >> number of
> >>                             atomtypes
> >> Ignoring obsolete mdp entry 'title'
> >> Ignoring obsolete mdp entry 'cpp'
> >> Back Off! I just backed up mdout.mdp to
> ./#mdout.mdp.2#
> >> checking input for internal consistency...
> >> processing topology...
> >> Opening library file
> >> /usr/local/md/share/gromacs/top/ffG53a6.itp
> >> Opening library file
> >> /usr/local/md/share/gromacs/top/ffG53a6nb.itp
> >> Opening library file
> >> /usr/local/md/share/gromacs/top/ffG53a6bon.itp
> >> Opening library file
> >> /usr/local/md/share/gromacs/top/ff_dum.itp
> >> WARNING 1 [file lipid.itp, line 14]:
> >>   Overriding atomtype LO
> >> WARNING 2 [file lipid.itp, line 15]:
> >>   Overriding atomtype LOM
> >> WARNING 3 [file lipid.itp, line 16]:
> >>   Overriding atomtype LNL
> >> WARNING 4 [file lipid.itp, line 17]:
> >>   Overriding atomtype LC
> >> WARNING 5 [file lipid.itp, line 18]:
> >>   Overriding atomtype LH1
> >> WARNING 6 [file lipid.itp, line 19]:
> >>   Overriding atomtype LH2
> >> WARNING 7 [file lipid.itp, line 20]:
> >>   Overriding atomtype LP
> >> WARNING 8 [file lipid.itp, line 21]:
> >>   Overriding atomtype LOS
> >> WARNING 9 [file lipid.itp, line 22]:
> >>   Overriding atomtype LP2
> >> WARNING 10 [file lipid.itp, line 23]:
> >>   Overriding atomtype LP3
> >> WARNING 11 [file lipid.itp, line 24]:
> >>   Overriding atomtype LC3
> >> WARNING 12 [file lipid.itp, line 25]:
> >>   Overriding atomtype LC2
> >> WARNING 13 [file lipid.itp, line 108]:
> >>   Overriding non-bonded parameters,
> >>   old: 0.00238804 3.38411e-06 new
> >> LNL     C   1   2.387718e-03 2.389594e-06
> >>
> -------------------------------------------------------
> >> Program grompp, VERSION 4.0
> >> Source code file: toppush.c, line: 793
> >> Fatal error:
> >> Atomtype CA not found
> >>
> >>
> >> -- 
> >> Jenny Hsu, Biotechnology Dept.,
> >> Ming Chuan University, Taiwan, R.O.C
> >> -------------- next part --------------
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> > 
> > 
> >       
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
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> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Fri, 28 Nov 2008 16:20:57 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] Box vector shifts number in x and
> y/z
> 	dimension
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <BAY122-W31A9F43C6D8128101902AD8E040 at phx.gbl>
> Content-Type: text/plain; charset="iso-2022-jp"
> 
> 
> Hi,
> 
> The b and c box vectors can be such that they both have as
> x component
> half the vector a x-length. Thus together they can cause a
> shift of 1 full
> x length and thus you might need 2 shifts along x.
> 
> Berk
> 
> > Date: Fri, 28 Nov 2008 09:41:31 +0800
> > From: xuji at home.ipe.ac.cn
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Box vector shifts number in x and
> y/z dimension
> > 
> > Hi all:
> > 
> > In gromacs all atoms are in the rectangular or
> triclinic unit-cell,
> > and in the codes using shifts with periodic boundary
> condition.
> > But why are there only single box vector shifts
> required in y and z dimensions 
> > but 2 in x dimension ?
> > 
> > Thanks for any help in advance!
> > 				 
> > $B!!!!!!!!!!!!!!!!(Bxuji
> > $B!!!!!!!!!!!!!!!!(Bxuji at home.ipe.ac.cn
> > $B!!!!!!!!!!!!!!!!!!!!(B2008-11-28
> > 
> 
> _________________________________________________________________
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