Hi Prof. Mark Abraham<br><br>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. <br><br>I will be very thankful if you introduce to me a tutorial about my work.<br>
<br>Thanks alot<br><br>Maria<br><br><div class="gmail_quote">On Mon, May 9, 2011 at 11:37 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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<br>
Today's Topics:<br>
<br>
1. regarding creating tabulated potentials (sreelakshmi ramesh)<br>
2. Re: Re: gmx-users Digest, Vol 85, Issue 61 (Mark Abraham)<br>
3. regarding nacl simulation in water using tabulated potentials<br>
(sreelakshmi ramesh)<br>
4. Re: RE: gmx-users Digest, Vol 85, Issue 53 (Mark Abraham)<br>
5. Re: regarding nacl simulation in water using tabulated<br>
potentials (Mark Abraham)<br>
6. Re: regarding nacl simulation in water using tabulated<br>
potentials (sreelakshmi ramesh)<br>
7. Re: regarding nacl simulation in water using tabulated<br>
potentials (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 9 May 2011 11:12:20 +0530<br>
From: sreelakshmi ramesh <<a href="mailto:sree.lakshmi@research.iiit.ac.in">sree.lakshmi@research.iiit.ac.in</a>><br>
Subject: [gmx-users] regarding creating tabulated potentials<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTimhMBkb0Ptt4wKCj_Dx=<a href="mailto:NBXwcQ-Qg@mail.gmail.com">NBXwcQ-Qg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
dear gmx users,<br>
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Message: 2<br>
Date: Mon, 09 May 2011 15:45:41 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 85, Issue 61<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DC77F85.8010709@anu.edu.au">4DC77F85.8010709@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 9/05/2011 3:40 PM, Maria Hamilton wrote:<br>
> Hi Dallas<br>
<br>
Please do not respond to whole digests - it confuses the archive. Cut<br>
out the relevant part and reply to it. Also, please choose a meaningful<br>
subject line.<br>
<br>
> You said that<br>
> "Easiest way is probably set up the appropriate sized box for molecule<br>
> 2, randomly distributed molecule 3 in appropriate number through it<br>
> (genbox), then solvate that box with molecule 2, then combine that box<br>
> with solvated box containing molecule 1."<br>
><br>
> How can I combine the two different box?Do you know any tutorial for this?<br>
<br>
Yes, the one on "biphasic systems" that I suggested two days ago that<br>
you search for :-)<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 9 May 2011 11:16:59 +0530<br>
From: sreelakshmi ramesh <<a href="mailto:sree.lakshmi@research.iiit.ac.in">sree.lakshmi@research.iiit.ac.in</a>><br>
Subject: [gmx-users] regarding nacl simulation in water using<br>
tabulated potentials<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTi=<a href="mailto:Upi92tu6DNjXM7oC9xfuk4HJYtw@mail.gmail.com">Upi92tu6DNjXM7oC9xfuk4HJYtw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
dear gmx users,<br>
i have to simulate nacl in water...the system is<br>
acubic box with just one na adn one cl ion in tip3p water.i wanted to use a<br>
buckingham potential for na adn cl interaction and lennard jones for water<br>
-ion intercation.i really dont have any idea on how to do this.any help will<br>
be of great use for me...<br>
<br>
thanks and regards,<br>
shree<br>
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<br>
Message: 4<br>
Date: Mon, 09 May 2011 15:47:55 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] RE: gmx-users Digest, Vol 85, Issue 53<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DC7800B.2080202@anu.edu.au">4DC7800B.2080202@anu.edu.au</a>><br>
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<br>
On 9/05/2011 9:10 AM, Ryan S Davis (rsdavis1) wrote:<br>
> I am not sure if I replied to this thread correctly, but anyway.<br>
<br>
Please use a relevant subject line.<br>
<br>
> I tried the things you guys suggested, but I still cant get it to work.<br>
> 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.<br>
<br>
Copy and paste of actual terminal sessions is always preferable.<br>
Computers are literal, and troubleshooting things filtered through<br>
people's heads usually wastes time.<br>
<br>
> I reinstalled the libraries, just to make sure everything went well.<br>
> So, here is what happens when I list out the library tree from my home directory and try to run the test code<br>
><br>
> $ ls -R /home/rsdavis1/apps/xdrfile/<br>
><br>
> /home/rsdavis1/apps/xdrfile/:<br>
> bin include lib<br>
><br>
> /home/rsdavis1/apps/xdrfile/bin:<br>
> trr2xtc<br>
><br>
> /home/rsdavis1/apps/xdrfile/include:<br>
> xdrfile<br>
><br>
> /home/rsdavis1/apps/xdrfile/include/xdrfile:<br>
> xdrfile.h xdrfile_trr.h xdrfile_xtc.h<br>
><br>
> /home/rsdavis1/apps/xdrfile/lib:<br>
> libxdrfile.a <a href="http://libxdrfile.la" target="_blank">libxdrfile.la</a><br>
><br>
> $<br>
> $<br>
> $ icpc -I/home/rsdavis1/apps/xdrfile/include/xdrfile/ -L/home/rsdavis1/apps/xdrfile/lib/ test.cpp -lxdrfile<br>
><br>
> /tmp/icpcUuD5jZ.o: In function `main':<br>
> test.cpp:(.text+0x33): undefined reference to `read_xtc_natoms(char*, int*)'<br>
> $<br>
<br>
That should work, so long as icpc doesn't need some weird invocation to<br>
look for non-shared libraries. Try<br>
<br>
/home/rsdavis1/apps/xdrfile/lib/libxdrfile.a<br>
<br>
instead of -lxdrfile<br>
<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Mon, 09 May 2011 15:50:26 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] regarding nacl simulation in water using<br>
tabulated potentials<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DC780A2.5010806@anu.edu.au">4DC780A2.5010806@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote:<br>
> dear gmx users,<br>
> i have to simulate nacl in water...the system<br>
> is acubic box with just one na adn one cl ion in tip3p water.i wanted<br>
> to use a buckingham potential for na adn cl interaction and lennard<br>
> jones for water -ion intercation.i really dont have any idea on how to<br>
> do this.any help will be of great use for me...<br>
<br>
Can't be done simply. You'd have to use non-bonded interaction tables<br>
for the Na-Cl interaction with properly constructed energy groups.<br>
Search the manual and webpage for details.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Mon, 9 May 2011 11:31:20 +0530<br>
From: sreelakshmi ramesh <<a href="mailto:sree.lakshmi@research.iiit.ac.in">sree.lakshmi@research.iiit.ac.in</a>><br>
Subject: Re: [gmx-users] regarding nacl simulation in water using<br>
tabulated potentials<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:BANLkTinfz7bGZo_RgTkgVstkD7gsg8fYhw@mail.gmail.com">BANLkTinfz7bGZo_RgTkgVstkD7gsg8fYhw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
i had followed the instructions in themnaual for ninbonded interactions adn<br>
had created two tables one for nacl adn other table for water ion<br>
interations...i wanted some information on how to use these tables for<br>
starting thee simulation<br>
<br>
On Mon, May 9, 2011 at 11:20 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>wrote:<br>
<br>
> On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote:<br>
><br>
>> dear gmx users,<br>
>> i have to simulate nacl in water...the system is<br>
>> acubic box with just one na adn one cl ion in tip3p water.i wanted to use a<br>
>> buckingham potential for na adn cl interaction and lennard jones for water<br>
>> -ion intercation.i really dont have any idea on how to do this.any help will<br>
>> be of great use for me...<br>
>><br>
><br>
> Can't be done simply. You'd have to use non-bonded interaction tables for<br>
> the Na-Cl interaction with properly constructed energy groups. Search the<br>
> manual and webpage for details.<br>
><br>
> Mark<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the www interface<br>
> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
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<br>
Message: 7<br>
Date: Mon, 09 May 2011 17:07:19 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] regarding nacl simulation in water using<br>
tabulated potentials<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DC792A7.70306@anu.edu.au">4DC792A7.70306@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote:<br>
> i had followed the instructions in themnaual for ninbonded<br>
> interactions adn had created two tables one for nacl adn other table<br>
> for water ion interations...<br>
<br>
That's not "I really don't have any idea on how to do this". Please ask<br>
the question you want answered, or you're wasting everyone's time.<br>
<br>
> i wanted some information on how to use these tables for starting thee<br>
> simulation<br>
<br>
Sorry, that's too general. You might want help with a command line, or<br>
setting up the .mdp, or something else. Please read 6.7 of the manual,<br>
try things, and ask a focused question.<br>
<br>
Mark<br>
<br>
> On Mon, May 9, 2011 at 11:20 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>
> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
><br>
> On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote:<br>
><br>
> dear gmx users,<br>
> i have to simulate nacl in water...the<br>
> system is acubic box with just one na adn one cl ion in tip3p<br>
> water.i wanted to use a buckingham potential for na adn cl<br>
> interaction and lennard jones for water -ion intercation.i<br>
> really dont have any idea on how to do this.any help will be<br>
> of great use for me...<br>
><br>
><br>
> Can't be done simply. You'd have to use non-bonded interaction<br>
> tables for the Na-Cl interaction with properly constructed energy<br>
> groups. Search the manual and webpage for details.<br>
><br>
> Mark<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the www<br>
> interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
><br>
<br>
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</font></blockquote></div><br>