[gmx-users] Re: gmx-users Digest, Vol 55, Issue 150
Justin A. Lemkul
jalemkul at vt.edu
Sat Nov 29 15:17:57 CET 2008
Q. Y. HUAN wrote:
> 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.
>
Well, as I suggested originally, the -cut option looks to be defining the
distance between you monomers to be considered aggregated. The default is 0.35
nm. It is possible then, for some monomers within 0.35 of each other, to
perhaps be considered in a cluster.
Are you also using -mol to look at clusters of molecules and not atoms?
-Justin
> 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
>>
>> 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: 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
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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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>
>
>
> _______________________________________________
> 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!
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> www interface or send it to gmx-users-request 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
========================================
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