[gmx-users] Re: Re: defination of cluster
Justin A. Lemkul
jalemkul at vt.edu
Fri Nov 28 13:29:12 CET 2008
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
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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
>>>
>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
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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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>> ------------------------------
>>
>> _______________________________________________
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>> End of gmx-users Digest, Vol 55, Issue 147
>> ******************************************
>
>
>
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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
========================================
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