Hi Dallas<br><br>You said that <br>"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."<br>
<br>How can I combine the two different box?Do you know any tutorial for this?<br><br>Thanks alot <br><br>Maria<br><br><div class="gmail_quote">On Mon, May 9, 2011 at 5:54 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;">Send gmx-users mailing list submissions to<br>
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<br>
Today's Topics:<br>
<br>
1. sphere around a protein (shivangi nangia)<br>
2. Re: sphere around a protein (Justin A. Lemkul)<br>
3. RE: gmx-users Digest, Vol 85, Issue 53 (Ryan S Davis (rsdavis1))<br>
4. RE: liquid/liquid (Dallas Warren)<br>
5. Re: sphere around a protein (shivangi nangia)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sun, 8 May 2011 16:13:33 -0400<br>
From: shivangi nangia <<a href="mailto:shivangi.nangia@gmail.com">shivangi.nangia@gmail.com</a>><br>
Subject: [gmx-users] sphere around a protein<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTin3xJKSGRLuckLhqba8YZ=<a href="mailto:MKVs1kA@mail.gmail.com">MKVs1kA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Justin and other gmx-users,<br>
<br>
I want to make a sphere around a protein (5nm).with Li ions and anions.<br>
<br>
Justin, as you had suggested to use genbox -shell option, I tried using it<br>
but i realized that since my protein is a long tube like structure, the<br>
shell option generated a cyclinder around the protein.<br>
<br>
The solvent around the protein is 1:1 water-methanol (pre-prepared mixture n<br>
a gro file)<br>
<br>
If I try to start with a ion and solvate it with my solvent (1:1 water<br>
methanol) using -shell option, I do get a sphere but then I am unable to<br>
insert the protein in the system.<br>
<br>
Is there another feasible route to get to my desired configuration of the<br>
system ?<br>
<br>
Thanks in advance<br>
<br>
<br>
Best,<br>
SN<br>
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<br>
Message: 2<br>
Date: Sun, 08 May 2011 17:12:33 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] sphere around a protein<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:4DC70741.8080209@vt.edu">4DC70741.8080209@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
shivangi nangia wrote:<br>
> Hi Justin and other gmx-users,<br>
><br>
> I want to make a sphere around a protein (5nm).with Li ions and anions.<br>
><br>
> Justin, as you had suggested to use genbox -shell option, I tried using<br>
> it but i realized that since my protein is a long tube like structure,<br>
> the shell option generated a cyclinder around the protein.<br>
><br>
> The solvent around the protein is 1:1 water-methanol (pre-prepared<br>
> mixture n a gro file)<br>
><br>
> If I try to start with a ion and solvate it with my solvent (1:1 water<br>
> methanol) using -shell option, I do get a sphere but then I am unable to<br>
> insert the protein in the system.<br>
><br>
<br>
And why not?<br>
<br>
genbox -cp protein.gro -cs sphere.gro<br>
<br>
should do exactly what you want, provided the sphere is large enough for the<br>
protein.<br>
<br>
-Justin<br>
<br>
> Is there another feasible route to get to my desired configuration of<br>
> the system ?<br>
><br>
> Thanks in advance<br>
><br>
><br>
> Best,<br>
> SN<br>
><br>
><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Sun, 8 May 2011 18:10:22 -0500<br>
From: "Ryan S Davis (rsdavis1)" <<a href="mailto:rsdavis1@memphis.edu">rsdavis1@memphis.edu</a>><br>
Subject: [gmx-users] RE: gmx-users Digest, Vol 85, Issue 53<br>
To: "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:6A7C9BBA12F23B478D0E40C0F6B8D4E87FCD23147C@itexbe11.uom.memphis.edu">6A7C9BBA12F23B478D0E40C0F6B8D4E87FCD23147C@itexbe11.uom.memphis.edu</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
I am not sure if I replied to this thread correctly, but anyway.<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>
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>
$<br>
<br>
<br>
<br>
and, again, test.cpp is just<br>
<br>
1 #include "xdrfile_xtc.h"<br>
2<br>
3 int main()<br>
4 {<br>
5<br>
6 int natoms;<br>
7 read_xtc_natoms("traj.xtc",&natoms);<br>
8 return 0;<br>
9<br>
10 }<br>
<br>
The compiler is finding the ".h" file from the include because when I specify the wrong function arguments, it complains about it.<br>
But, I guess it still isnt seeing the library.<br>
Also, I tried compiling after appending the LIBDIR to my LD_LIBRARY_PATH and LD_RUN_PATH, neither worked.<br>
<br>
<br>
Message: 1<br>
Date: Fri, 6 May 2011 22:31:23 -0500<br>
From: "Ryan S Davis (rsdavis1)" <<a href="mailto:rsdavis1@memphis.edu">rsdavis1@memphis.edu</a>><br>
Subject: [gmx-users] Using the XTC library<br>
To: "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:6A7C9BBA12F23B478D0E40C0F6B8D4E87FCD231479@itexbe11.uom.memphis.edu">6A7C9BBA12F23B478D0E40C0F6B8D4E87FCD231479@itexbe11.uom.memphis.edu</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
I am trying to use the XTC library in my code but I am just not good at this stuff.<br>
<a href="http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library" target="_blank">http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library</a><br>
<br>
<br>
I installed using<br>
./configure --prefix=/$HOME/apps/xdrfile<br>
make install<br>
<br>
everything seemed to go well and the make check said everything passed.<br>
<br>
So then I try a test code<br>
<br>
1 #include <iostream><br>
2 #include "xdrfile_xtc.h"<br>
3 using namespace std;<br>
4<br>
5 int main()<br>
6 {<br>
7<br>
8 int natoms;<br>
9 read_xtc_natoms("traj.xtc", &natoms);<br>
10 return 0;<br>
11 }<br>
<br>
and I compile with<br>
<br>
icc -I/$HOME/apps/xdrfile/include/xdrfile -L/$HOME/apps/xdrfile/lib/ test.cpp<br>
<br>
and i get an error saying...<br>
<br>
undefined reference to 'read_xtc_natoms(char *, int*)'<br>
<br>
I am sure that I am doing something stupid. I tried a C compiler and linking to few other random places but, like I said, this stuff (installing libraries and linking) is new to me.<br>
Please help.<br>
<br>
Thanks<br>
Ryan<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Sat, 07 May 2011 13:55:26 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Using the XTC library<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:4DC4C2AE.6090505@anu.edu.au">4DC4C2AE.6090505@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 7/05/2011 1:31 PM, Ryan S Davis (rsdavis1) wrote:<br>
> I am trying to use the XTC library in my code but I am just not good at this stuff.<br>
> <a href="http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library" target="_blank">http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library</a><br>
><br>
><br>
> I installed using<br>
> ./configure --prefix=/$HOME/apps/xdrfile<br>
<br>
This might not be the problem, but the HOME environment variable here<br>
and below will normally start with a slash, and so you should not<br>
preface it with another.<br>
<br>
> make install<br>
><br>
> everything seemed to go well and the make check said everything passed.<br>
><br>
> So then I try a test code<br>
><br>
> 1 #include<iostream><br>
> 2 #include "xdrfile_xtc.h"<br>
> 3 using namespace std;<br>
> 4<br>
> 5 int main()<br>
> 6 {<br>
> 7<br>
> 8 int natoms;<br>
> 9 read_xtc_natoms("traj.xtc",&natoms);<br>
> 10 return 0;<br>
> 11 }<br>
><br>
> and I compile with<br>
><br>
> icc -I/$HOME/apps/xdrfile/include/xdrfile -L/$HOME/apps/xdrfile/lib/ test.cpp<br>
><br>
> and i get an error saying...<br>
><br>
> undefined reference to 'read_xtc_natoms(char *, int*)'<br>
><br>
> I am sure that I am doing something stupid. I tried a C compiler and linking to few other random places but, like I said, this stuff (installing libraries and linking) is new to me.<br>
> Please help.<br>
<br>
icc -I$HOME/apps/xdrfile/include/xdrfile test.cpp<br>
<br>
will find $HOME/apps/xdrfile/include/xdrfile/xdrfile_xtc.h<br>
<br>
Mark<br>
<br>
<br>
<br>
<br>
Message: 4<br>
Date: Fri, 06 May 2011 22:22:04 -0700<br>
From: "Joshua L. Phillips" <<a href="mailto:jphillips7@ucmerced.edu">jphillips7@ucmerced.edu</a>><br>
Subject: Re: [gmx-users] Using the XTC library<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:1304745725.16113.32.camel@onesiphorus.mercedcapoeira.com">1304745725.16113.32.camel@onesiphorus.mercedcapoeira.com</a>><br>
Content-Type: text/plain; charset="UTF-8"<br>
<br>
You will need to link with the library as well (-lxdrfile)<br>
<br>
Something like the following should work (if the paths that you provided<br>
are correct):<br>
<br>
icpc -I$HOME/apps/xdrfile/include/xdrfile \<br>
-L$HOME/apps/xdrfile/lib test.cpp -o test -lxdrfile<br>
<br>
(Since, this is C++ code, then you should be using icpc instead of<br>
icc...)<br>
<br>
-- Josh<br>
<br>
On Sat, 2011-05-07 at 13:55 +1000, Mark Abraham wrote:<br>
> On 7/05/2011 1:31 PM, Ryan S Davis (rsdavis1) wrote:<br>
> > I am trying to use the XTC library in my code but I am just not good at this stuff.<br>
> > <a href="http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library" target="_blank">http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library</a><br>
> ><br>
> ><br>
> > I installed using<br>
> > ./configure --prefix=/$HOME/apps/xdrfile<br>
><br>
> This might not be the problem, but the HOME environment variable here<br>
> and below will normally start with a slash, and so you should not<br>
> preface it with another.<br>
><br>
> > make install<br>
> ><br>
> > everything seemed to go well and the make check said everything passed.<br>
> ><br>
> > So then I try a test code<br>
> ><br>
> > 1 #include<iostream><br>
> > 2 #include "xdrfile_xtc.h"<br>
> > 3 using namespace std;<br>
> > 4<br>
> > 5 int main()<br>
> > 6 {<br>
> > 7<br>
> > 8 int natoms;<br>
> > 9 read_xtc_natoms("traj.xtc",&natoms);<br>
> > 10 return 0;<br>
> > 11 }<br>
> ><br>
> > and I compile with<br>
> ><br>
> > icc -I/$HOME/apps/xdrfile/include/xdrfile -L/$HOME/apps/xdrfile/lib/ test.cpp<br>
> ><br>
> > and i get an error saying...<br>
> ><br>
> > undefined reference to 'read_xtc_natoms(char *, int*)'<br>
> ><br>
> > I am sure that I am doing something stupid. I tried a C compiler and linking to few other random places but, like I said, this stuff (installing libraries and linking) is new to me.<br>
> > Please help.<br>
><br>
> icc -I$HOME/apps/xdrfile/include/xdrfile test.cpp<br>
><br>
> will find $HOME/apps/xdrfile/include/xdrfile/xdrfile_xtc.h<br>
><br>
> Mark<br>
<br>
--<br>
Joshua L. Phillips<br>
Ph.D. Candidate - School of Engineering<br>
University of California, Merced<br>
<a href="mailto:jphillips7@ucmerced.edu">jphillips7@ucmerced.edu</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Sun, 08 May 2011 23:51:40 +0000<br>
From: Dallas Warren <<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>><br>
Subject: RE: [gmx-users] liquid/liquid<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<F625AF4746B3A74DACFF00F6F65BECCB0C8E4066@vPRK-MBX-01.vcp.local><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
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.<br>
<br>
Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Medicinal Chemistry and Drug Action<br>
Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu">dallas.warren@monash.edu</a><br>
+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.<br>
<br>
From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] On Behalf Of Maria Hamilton<br>
Sent: Saturday, 7 May 2011 6:04 PM<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] liquid/liquid<br>
<br>
Hi all<br>
<br>
I want to simulate a liquid/liquid interface. After construction one of them in one side of the box and the other in the another side, I want to all some other molecules randomly in one of them. What should I do?<br>
<br>
Would you please help me?<br>
<br>
Thanks alot<br>
<br>
Maria<br>
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<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Sun, 8 May 2011 21:23:26 -0400<br>
From: shivangi nangia <<a href="mailto:shivangi.nangia@gmail.com">shivangi.nangia@gmail.com</a>><br>
Subject: Re: [gmx-users] sphere around a protein<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:BANLkTimbHghPcBz6nBUHnBU83t-frDUaEQ@mail.gmail.com">BANLkTimbHghPcBz6nBUHnBU83t-frDUaEQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello,<br>
<br>
Thanks Justin, I am getting somewhere but still running into problems.<br>
<br>
Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 water-methanol<br>
mixture) in 12 nm box.<br>
I did the following:<br>
editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro<br>
genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro<br>
<br>
<br>
Then, used genbox -cp protein.gro -cs sphere.gro<br>
with only 1 molecule of histidine I get the same error as with polyhistidine<br>
( 20 )<br>
<br>
Fatal error:<br>
One of the box vectors has become shorter than twice the cut-off length or<br>
box_yy-|box_zy| or box_zz has become smaller than the cut-off.<br>
<br>
How can I resolve this?<br>
<br>
help needed.<br>
<br>
Thanks,<br>
SN<br>
<br>
On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<br>
><br>
><br>
> shivangi nangia wrote:<br>
><br>
>> Hi Justin and other gmx-users,<br>
>><br>
>> I want to make a sphere around a protein (5nm).with Li ions and anions.<br>
>><br>
>> Justin, as you had suggested to use genbox -shell option, I tried using it<br>
>> but i realized that since my protein is a long tube like structure, the<br>
>> shell option generated a cyclinder around the protein.<br>
>><br>
>> The solvent around the protein is 1:1 water-methanol (pre-prepared mixture<br>
>> n a gro file)<br>
>><br>
>> If I try to start with a ion and solvate it with my solvent (1:1 water<br>
>> methanol) using -shell option, I do get a sphere but then I am unable to<br>
>> insert the protein in the system.<br>
>><br>
>><br>
> And why not?<br>
><br>
> genbox -cp protein.gro -cs sphere.gro<br>
><br>
> should do exactly what you want, provided the sphere is large enough for<br>
> the protein.<br>
><br>
> -Justin<br>
><br>
><br>
> Is there another feasible route to get to my desired configuration of the<br>
>> system ?<br>
>><br>
>> Thanks in advance<br>
>><br>
>><br>
>> Best,<br>
>> SN<br>
>><br>
>><br>
>><br>
>><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> --<br>
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End of gmx-users Digest, Vol 85, Issue 61<br>
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