[gmx-users] Re: gmx-users Digest, Vol 85, Issue 65
Maria Hamilton
hamilton.maria39 at gmail.com
Mon May 9 13:55:56 CEST 2011
Hi Prof. Mark Abraham
I recived a tutorial from you that in the tutorial 3th molecule was one and
there is not some of the 3th molecules that distributed randomly.
I will be very thankful if you introduce to me a tutorial about my work.
Thanks alot
Maria
On Mon, May 9, 2011 at 11:37 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. regarding creating tabulated potentials (sreelakshmi ramesh)
> 2. Re: Re: gmx-users Digest, Vol 85, Issue 61 (Mark Abraham)
> 3. regarding nacl simulation in water using tabulated potentials
> (sreelakshmi ramesh)
> 4. Re: RE: gmx-users Digest, Vol 85, Issue 53 (Mark Abraham)
> 5. Re: regarding nacl simulation in water using tabulated
> potentials (Mark Abraham)
> 6. Re: regarding nacl simulation in water using tabulated
> potentials (sreelakshmi ramesh)
> 7. Re: regarding nacl simulation in water using tabulated
> potentials (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 9 May 2011 11:12:20 +0530
> From: sreelakshmi ramesh <sree.lakshmi at research.iiit.ac.in>
> Subject: [gmx-users] regarding creating tabulated potentials
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTimhMBkb0Ptt4wKCj_Dx=NBXwcQ-Qg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> dear gmx users,
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> ------------------------------
>
> Message: 2
> Date: Mon, 09 May 2011 15:45:41 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 85, Issue 61
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DC77F85.8010709 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 9/05/2011 3:40 PM, Maria Hamilton wrote:
> > Hi Dallas
>
> Please do not respond to whole digests - it confuses the archive. Cut
> out the relevant part and reply to it. Also, please choose a meaningful
> subject line.
>
> > You said that
> > "Easiest way is probably set up the appropriate sized box for molecule
> > 2, randomly distributed molecule 3 in appropriate number through it
> > (genbox), then solvate that box with molecule 2, then combine that box
> > with solvated box containing molecule 1."
> >
> > How can I combine the two different box?Do you know any tutorial for
> this?
>
> Yes, the one on "biphasic systems" that I suggested two days ago that
> you search for :-)
>
> Mark
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 9 May 2011 11:16:59 +0530
> From: sreelakshmi ramesh <sree.lakshmi at research.iiit.ac.in>
> Subject: [gmx-users] regarding nacl simulation in water using
> tabulated potentials
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTi=Upi92tu6DNjXM7oC9xfuk4HJYtw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> dear gmx users,
> i have to simulate nacl in water...the system is
> acubic box with just one na adn one cl ion in tip3p water.i wanted to use a
> buckingham potential for na adn cl interaction and lennard jones for water
> -ion intercation.i really dont have any idea on how to do this.any help
> will
> be of great use for me...
>
> thanks and regards,
> shree
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> ------------------------------
>
> Message: 4
> Date: Mon, 09 May 2011 15:47:55 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] RE: gmx-users Digest, Vol 85, Issue 53
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DC7800B.2080202 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 9/05/2011 9:10 AM, Ryan S Davis (rsdavis1) wrote:
> > I am not sure if I replied to this thread correctly, but anyway.
>
> Please use a relevant subject line.
>
> > I tried the things you guys suggested, but I still cant get it to work.
> > You were right $HOME does have a slash in front but I am not actually
> using that variable, just used it in the mailing list for convience, sorry.
>
> Copy and paste of actual terminal sessions is always preferable.
> Computers are literal, and troubleshooting things filtered through
> people's heads usually wastes time.
>
> > I reinstalled the libraries, just to make sure everything went well.
> > So, here is what happens when I list out the library tree from my home
> directory and try to run the test code
> >
> > $ ls -R /home/rsdavis1/apps/xdrfile/
> >
> > /home/rsdavis1/apps/xdrfile/:
> > bin include lib
> >
> > /home/rsdavis1/apps/xdrfile/bin:
> > trr2xtc
> >
> > /home/rsdavis1/apps/xdrfile/include:
> > xdrfile
> >
> > /home/rsdavis1/apps/xdrfile/include/xdrfile:
> > xdrfile.h xdrfile_trr.h xdrfile_xtc.h
> >
> > /home/rsdavis1/apps/xdrfile/lib:
> > libxdrfile.a libxdrfile.la
> >
> > $
> > $
> > $ icpc -I/home/rsdavis1/apps/xdrfile/include/xdrfile/
> -L/home/rsdavis1/apps/xdrfile/lib/ test.cpp -lxdrfile
> >
> > /tmp/icpcUuD5jZ.o: In function `main':
> > test.cpp:(.text+0x33): undefined reference to
> `read_xtc_natoms(char*, int*)'
> > $
>
> That should work, so long as icpc doesn't need some weird invocation to
> look for non-shared libraries. Try
>
> /home/rsdavis1/apps/xdrfile/lib/libxdrfile.a
>
> instead of -lxdrfile
>
>
> Mark
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 09 May 2011 15:50:26 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] regarding nacl simulation in water using
> tabulated potentials
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DC780A2.5010806 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote:
> > dear gmx users,
> > i have to simulate nacl in water...the system
> > is acubic box with just one na adn one cl ion in tip3p water.i wanted
> > to use a buckingham potential for na adn cl interaction and lennard
> > jones for water -ion intercation.i really dont have any idea on how to
> > do this.any help will be of great use for me...
>
> Can't be done simply. You'd have to use non-bonded interaction tables
> for the Na-Cl interaction with properly constructed energy groups.
> Search the manual and webpage for details.
>
> Mark
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 9 May 2011 11:31:20 +0530
> From: sreelakshmi ramesh <sree.lakshmi at research.iiit.ac.in>
> Subject: Re: [gmx-users] regarding nacl simulation in water using
> tabulated potentials
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTinfz7bGZo_RgTkgVstkD7gsg8fYhw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> i had followed the instructions in themnaual for ninbonded interactions adn
> had created two tables one for nacl adn other table for water ion
> interations...i wanted some information on how to use these tables for
> starting thee simulation
>
> On Mon, May 9, 2011 at 11:20 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> >wrote:
>
> > On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote:
> >
> >> dear gmx users,
> >> i have to simulate nacl in water...the system is
> >> acubic box with just one na adn one cl ion in tip3p water.i wanted to
> use a
> >> buckingham potential for na adn cl interaction and lennard jones for
> water
> >> -ion intercation.i really dont have any idea on how to do this.any help
> will
> >> be of great use for me...
> >>
> >
> > Can't be done simply. You'd have to use non-bonded interaction tables for
> > the Na-Cl interaction with properly constructed energy groups. Search the
> > manual and webpage for details.
> >
> > Mark
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
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> ------------------------------
>
> Message: 7
> Date: Mon, 09 May 2011 17:07:19 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] regarding nacl simulation in water using
> tabulated potentials
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DC792A7.70306 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote:
> > i had followed the instructions in themnaual for ninbonded
> > interactions adn had created two tables one for nacl adn other table
> > for water ion interations...
>
> That's not "I really don't have any idea on how to do this". Please ask
> the question you want answered, or you're wasting everyone's time.
>
> > i wanted some information on how to use these tables for starting thee
> > simulation
>
> Sorry, that's too general. You might want help with a command line, or
> setting up the .mdp, or something else. Please read 6.7 of the manual,
> try things, and ask a focused question.
>
> Mark
>
> > On Mon, May 9, 2011 at 11:20 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> > <mailto:Mark.Abraham at anu.edu.au>> wrote:
> >
> > On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote:
> >
> > dear gmx users,
> > i have to simulate nacl in water...the
> > system is acubic box with just one na adn one cl ion in tip3p
> > water.i wanted to use a buckingham potential for na adn cl
> > interaction and lennard jones for water -ion intercation.i
> > really dont have any idea on how to do this.any help will be
> > of great use for me...
> >
> >
> > Can't be done simply. You'd have to use non-bonded interaction
> > tables for the Na-Cl interaction with properly constructed energy
> > groups. Search the manual and webpage for details.
> >
> > Mark
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/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
> > <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
>
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> End of gmx-users Digest, Vol 85, Issue 65
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>
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