[gmx-users] Re: Re: defination of cluster
Q. Y. HUAN
scottiehuan at yahoo.com
Fri Nov 28 09:25:14 CET 2008
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.
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
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> 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
> >
> >
> >
> > _______________________________________________
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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
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