I had tried the same for single node as -np 1 in my local m/c.<br><br>BR<br><br><div class="gmail_quote">On Fri, Apr 18, 2008 at 6:33 AM, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Send gmx-users mailing list submissions to<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of gmx-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. GDB Debugging - GROMACS(v-3.3.3) Application with<br>
OpenMPI(v-1.2.5/v-1.2.6) (Mukesh K Srivastava)<br>
2. Re: GDB Debugging - GROMACS(v-3.3.3) Application with<br>
OpenMPI(v-1.2.5/v-1.2.6) (David van der Spoel)<br>
3. Re: epsilon in mdp (David van der Spoel)<br>
4. Conformation search! (Anthony Cruz)<br>
5. Re: query about .xpm file (David van der Spoel)<br>
6. water flow in CNT (Hero)<br>
7. water in channel by "Dowser" (Hero)<br>
8. Re: dielectric constant (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 17 Apr 2008 23:06:50 +0530<br>
From: "Mukesh K Srivastava" <<a href="mailto:srimks11@gmail.com">srimks11@gmail.com</a>><br>
Subject: [gmx-users] GDB Debugging - GROMACS(v-3.3.3) Application with<br>
OpenMPI(v-1.2.5/v-1.2.6)<br>
To: <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>, <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Cc: <a href="mailto:gmx-announce@gromacs.org">gmx-announce@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:3efa6bfc0804171036y26bce920vdb332fed3837f675@mail.gmail.com">3efa6bfc0804171036y26bce920vdb332fed3837f675@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi.<br>
<br>
Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3) application<br>
with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had properly configured<br>
OpenMPI with debug option and also configured Gromacs alongwith FFTW<br>
succesfully. I can perform p2bdbx_mpi, editconf_mpi, genbox_mpi, grompp_mpi<br>
compilation and finally mdrun_mpi without any error or warning messages. But<br>
while executing mdrun_mpi w.r.t mprun, I get libmpi.so.0 not found.<br>
<br>
I had tried with LD_LIBRARY_PATH, forcefully mentioning PATH &<br>
LD_LIBRARY_PATH in etc/bashrc file and also tried with providing softlink to<br>
libmpi.so.0, but everytime I get same error message of "libmpi.so.0" not<br>
found.<br>
<br>
I had check ldd and it's dependency of executable mdrun_mpi, checked it's<br>
symbol table content, and finally all lib's configured for 64 bit with ELF<br>
format but still getting same error of libmpi.so.0 not found while<br>
performing GDB serial debugging with single node.<br>
<br>
Note: I had performed GDB debugging for small MPI program(hello world) using<br>
OpenMPI(v1.2.5/v1.2.6) wthout GROMACS association succesfully.<br>
<br>
Any clue plz?<br>
<br>
BR<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20080417/6b05965e/attachment-0001.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20080417/6b05965e/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 17 Apr 2008 20:51:52 +0200<br>
From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] GDB Debugging - GROMACS(v-3.3.3) Application<br>
with OpenMPI(v-1.2.5/v-1.2.6)<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:48079C48.5040901@xray.bmc.uu.se">48079C48.5040901@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Mukesh K Srivastava wrote:<br>
> Hi.<br>
><br>
> Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3)<br>
> application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had<br>
> properly configured OpenMPI with debug option and also configured<br>
> Gromacs alongwith FFTW succesfully. I can perform p2bdbx_mpi,<br>
> editconf_mpi, genbox_mpi, grompp_mpi compilation and finally mdrun_mpi<br>
> without any error or warning messages. But while executing mdrun_mpi<br>
> w.r.t mprun, I get libmpi.so.0 not found.<br>
><br>
> I had tried with LD_LIBRARY_PATH, forcefully mentioning PATH &<br>
> LD_LIBRARY_PATH in etc/bashrc file and also tried with providing<br>
> softlink to libmpi.so.0, but everytime I get same error message of<br>
> "libmpi.so.0" not found.<br>
><br>
> I had check ldd and it's dependency of executable mdrun_mpi, checked<br>
> it's symbol table content, and finally all lib's configured for 64 bit<br>
> with ELF format but still getting same error of libmpi.so.0 not found<br>
> while performing GDB serial debugging with single node.<br>
><br>
> Note: I had performed GDB debugging for small MPI program(hello<br>
> world) using OpenMPI(v1.2.5/v1.2.6) wthout GROMACS association succesfully.<br>
><br>
> Any clue plz?<br>
try<br>
ldd mdrun_mpi<br>
on the nodes. probably the mpi is not installed on the nodes.<br>
<br>
><br>
> BR<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface 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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
--<br>
David.<br>
________________________________________________________________________<br>
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: 46 18 471 4205 fax: 46 18 511 755<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 17 Apr 2008 20:52:36 +0200<br>
From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] epsilon in mdp<br>
To: Vitaly Chaban <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>>, Discussion list for GROMACS<br>
users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:48079C74.20501@xray.bmc.uu.se">48079C74.20501@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Vitaly Chaban wrote:<br>
> Dear gromacs users,<br>
><br>
> In the gromacs example mdp-file for water (/tutor/water) one can find<br>
> "<br>
> ; Dielectric constant (DC) for cut-off or DC of reaction field<br>
> epsilon-r = 1<br>
> "<br>
><br>
> Does it mean that the simulation will be hold as if DC of H2O were<br>
> equal to the DC of vacuum? Does one need to correct it to the<br>
> corresponding experimental value for water to obtain a real system?<br>
><br>
<br>
<br>
this is outdated. sorry about that. check onlin documentation.<br>
<br>
> Thanks,<br>
> Vitaly<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface 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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
--<br>
David.<br>
________________________________________________________________________<br>
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: 46 18 471 4205 fax: 46 18 511 755<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 17 Apr 2008 15:31:08 -0400<br>
From: Anthony Cruz <<a href="mailto:acb15885@uprm.edu">acb15885@uprm.edu</a>><br>
Subject: [gmx-users] Conformation search!<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:200804171531.08356.acb15885@uprm.edu">200804171531.08356.acb15885@uprm.edu</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi User:<br>
We have a protein with two domains. This two domains were connected by two<br>
linkers of different length. We want to study the different conformation that<br>
the protein domains can adopt depending the length of the linkers without<br>
loosing the secondary structure feature present. I was thinking in use some<br>
position restrain in the backbone atoms of the domains and leave the linkers<br>
and all the side chains to move freely but this aproach will not let the<br>
system to change the conformation.<br>
I'm using GROMACS <a href="http://3.2.1." target="_blank">3.2.1.</a><br>
With a dihedral constraint it will be posible to what I want to do?<br>
How can I do it?<br>
There is any other option to do this?<br>
<br>
Best Regards,<br>
Anthony<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Thu, 17 Apr 2008 22:26:49 +0200<br>
From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] query about .xpm file<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:4807B289.8080408@xray.bmc.uu.se">4807B289.8080408@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
Bert wrote:<br>
> Hi gmx-usrs,<br>
><br>
> I use the program g_densmap to generate a xpm file, and then I convert<br>
> it to eps format with xpm2ps. It goes quite well except for the<br>
> illegible coordinates with the ticks. I wonder if I can set those<br>
> coodinates arbitrarily. I have tried to adjust the -bx, -by set and the<br>
> m2p input file, but I can not set the coordinates of the ticks with<br>
> regular integers. Thanks very much for suggestions.<br>
<br>
Apart from the options in the m2p file, you can also edit the xpm file,<br>
because the legends are in there.<br>
><br>
> Bert<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface 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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
--<br>
David van der Spoel, Ph.D.<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Thu, 17 Apr 2008 16:16:18 -0700 (PDT)<br>
From: Hero <<a href="mailto:cjt0610@yahoo.com">cjt0610@yahoo.com</a>><br>
Subject: [gmx-users] water flow in CNT<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:438078.70334.qm@web32503.mail.mud.yahoo.com">438078.70334.qm@web32503.mail.mud.yahoo.com</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Dear All,<br>
<br>
I am simulating water transport in CNT under pressure.<br>
<br>
If I use periodic boundary conditions, how can I scale the<br>
water velocity? Otherwise the velocity will be going to heaven!<br>
<br>
Thank you very much!<br>
<br>
Hero<br>
<br>
<br>
____________________________________________________________________________________<br>
Be a better friend, newshound, and<br>
know-it-all with Yahoo! Mobile. Try it now. <a href="http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ" target="_blank">http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Thu, 17 Apr 2008 17:17:55 -0700 (PDT)<br>
From: Hero <<a href="mailto:cjt0610@yahoo.com">cjt0610@yahoo.com</a>><br>
Subject: [gmx-users] water in channel by "Dowser"<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:883544.65024.qm@web32506.mail.mud.yahoo.com">883544.65024.qm@web32506.mail.mud.yahoo.com</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Dear Gramacs,<br>
<br>
Anybody know where I can get "Dowser" for water in channel?<br>
<br>
Thanks a lot!<br>
<br>
[gmx-users] water in channel<br>
Eric Jakobsson jake at <a href="http://ncsa.uiuc.edu" target="_blank">ncsa.uiuc.edu</a><br>
Mon Jan 19 22:50:02 CET 2004<br>
Previous message: [gmx-users] water in channel<br>
Next message: [gmx-users] water in channel<br>
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]<br>
<br>
<br>
<br>
Approach # 2) will not work for all channels. We published a paper in<br>
Biophys. J. a number of years ago in which we looked at water motion in<br>
the gramicidin channel with the protein immobile but the water at 300<br>
K. The water moved locally in the normal way, but had no motion along the<br>
channel at all. I am sure if we had started with the channel empty and<br>
the gramicidin frozen, it would never have filled, at least not in any<br>
reasonable time. On the other hand, for some channels if you don't<br>
immobilize them and you don't have contents in the lumen, the lumenal<br>
structure will become unstable. So approach # 1) (Dowser or some<br>
equivalent method) is the better way, based on our group's experience.<br>
<br>
Eric<br>
<br>
At 11:31 AM 1/19/2004 -0500, you wrote:<br>
<br>
>I can think of 2 options:<br>
><br>
>1) There is a program called "Dowser" put out by J. Hermans' lab at<br>
>UNC-Chapel hill. It usually works very well.<br>
><br>
>2) You can position restrain the channel and allow water and bilayer to<br>
>move freely during MD. It should not take long for water to enter the<br>
>channel ... that is, providing that it is actually supposed to do so. Water<br>
>is probably the fastest diffusing species in your system. You can take<br>
>advantage of this.<br>
><br>
>David<br>
><br>
>-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=<br>
>David Bostick Office: 262 Venable Hall<br>
>Dept. of Physics and Astronomy Phone: (919)962-0165<br>
>Program in Molecular and Cellular Biophysics<br>
>UNC-Chapel Hill<br>
>CB #3255 Phillips Hall dbostick at <a href="http://physics.unc.edu" target="_blank">physics.unc.edu</a><br>
>Chapel Hill, NC 27599 <a href="http://www.unc.edu/%7Edbostick" target="_blank">http://www.unc.edu/~dbostick</a><br>
>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-<br>
><br>
>On Mon, 19 Jan 2004, Itamar Kass wrote:<br>
><br>
> > Hi all, I am currently working on a channel in a DMPC bilayer (and<br>
> water). After inserting the channel into the bilayer (using Graham's<br>
> modified mdrun) I am facing a new problem. I want to put water in the<br>
> channel and did not succeed in doing it. Using pr simulation I did not<br>
> succeed, then I tried to use genbox, but it puts water in the membrane also.<br>
> > Does someone have an idea or face it and has a solution?<br>
> > Thank you, Itamar.<br>
> ><br>
> > ********************************************<br>
> > Computers are like airconditioners... They don't work well with Windows<br>
> open.<br>
> > ********************************************<br>
> ><br>
> > ===========================================<br>
> > | Itamar Kass<br>
> > | The Alexander Silberman<br>
> > | Institute of Life Sciences<br>
> > | Department of Biological Chemistry<br>
> > | The Hebrew University, Givat-Ram<br>
> > | Jerusalem, 91904, Israel<br>
> > | Tel: +972-(0)2-6585146<br>
> > | Fax: +972-(0)2-6584329<br>
> > | Email: ikass at <a href="http://cc.huji.ac.il" target="_blank">cc.huji.ac.il</a><br>
> > | Homepage:<br>
> <a href="http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html" target="_blank">http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html</a><br>
> > ============================================<br>
><br>
>_______________________________________________<br>
>gmx-users mailing list<br>
>gmx-users at <a href="http://gromacs.org" target="_blank">gromacs.org</a><br>
><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
>Please don't post (un)subscribe requests to the list. Use the<br>
>www interface or send it to gmx-users-request at <a href="http://gromacs.org" target="_blank">gromacs.org</a>.<br>
<br>
---------------------------------<br>
Eric Jakobsson, Ph.D.<br>
Professor, Department of Molecular and Integrative Physiology, and of<br>
Biochemistry<br>
Senior Research Scientist, National Center for Supercomputing Applications<br>
Professor, Beckman Institute for Advanced Science and Technology<br>
4021 Beckman Institute, mc251<br>
University of Illinois, Urbana, IL 61801<br>
ph. 217-244-2896 fax 217-244-2909<br>
(Currently on leave to the National Institutes of Health in Bethesda,<br>
Maryland, to be Director of the NIGMS Center for Bioinformatics and<br>
Computational Biology and Chair of the NIH Biomedical Information Science<br>
and Technology Initiative Consortium, but maintaining my research lab at<br>
Illinois by periodic commuting. My usual schedule is four days a week at<br>
NIH and three days a week at Illinois.)<br>
<br>
<br>
____________________________________________________________________________________<br>
Be a better friend, newshound, and<br>
know-it-all with Yahoo! Mobile. Try it now. <a href="http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ" target="_blank">http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 8<br>
Date: Fri, 18 Apr 2008 11:02:27 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] dielectric constant<br>
To: Gromacs Users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4807F323.1080604@anu.edu.au">4807F323.1080604@anu.edu.au</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<a href="mailto:gadies@fh.huji.ac.il">gadies@fh.huji.ac.il</a> wrote:<br>
> Dear Mark,<br>
<br>
Please leave traffic on the list for all to learn from and so that the<br>
conversation gets archived.<br>
<br>
> Is there somewhere I can read about this?<br>
<br>
Not that I know of.<br>
<br>
> Do you have an example of a similar simulation that has been done?<br>
<br>
No. I was commenting based on my GROMACS experience, not my experience<br>
of your intended problem type.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
<br>
End of gmx-users Digest, Vol 48, Issue 54<br>
*****************************************<br>
</blockquote></div><br>