<div><br>Dear Justin,</div>
<div> I did make the rtp and hdb files in accordance with the tutorial onthe website <a href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html" target="_blank"><font color="#1e5494"><a href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html,but">http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html</a></font></a>,but the problem cann't be settle,what can I do?</div>
<div> Looking forward for your reply!</div>
<div> Thanks,</div>
<div> dreamcatcher<br></div>
<div class="gmail_quote">On Tue, Aug 25, 2009 at 2:57 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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<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. Re: [Fwd: Please solve my problem] (<a href="mailto:cesteban@unsl.edu.ar">cesteban@unsl.edu.ar</a>)<br>
2. Something about getting started (DreamCatcher)<br> 3. Re: Something about getting started (Justin A. Lemkul)<br> 4. Re: correlation function (Jamie Seyed)<br><br><br>----------------------------------------------------------------------<br>
<br>Message: 1<br>Date: Mon, 24 Aug 2009 10:30:45 -0400 (ARGSL-DT)<br>From: <a href="mailto:cesteban@unsl.edu.ar">cesteban@unsl.edu.ar</a><br>Subject: Re: [gmx-users] [Fwd: Please solve my problem]<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:<br> <<a href="mailto:51938.64.76.125.131.1251124245.squirrel@webmail2.unsl.edu.ar">51938.64.76.125.131.1251124245.squirrel@webmail2.unsl.edu.ar</a>><br>
Content-Type: text/plain;charset=iso-8859-1<br><br>Hi again<br>the MPI coding is OPEN MPI 1.2.7 that is found in the ROCKS CLUSTER 5.1<br>distribution<br>thanks<br>Carmen<br>><br>> <a href="mailto:cesteban@unsl.edu.ar">cesteban@unsl.edu.ar</a> wrote:<br>
>> Hi All<br>>> I have similar problem using gromacs 4.0.2.<br>>> The MD simulation (5 ns) on single processor is complited in 5 days, but<br>>> the same MD can`t be complited on cluster on 4 or 8 processors. The MD<br>
>> simulation is stopped without any error message.<br>>> Any help would be appreciated<br>><br>> Which MPI implementation are you using? Some are known to be buggy.<br>> Also, to<br>> rule out any other potentially buggy behavior, upgrade to version 4.0.5;<br>
> 4.0.2<br>> is several months old.<br>><br>> -Justin<br>><br>>> Carmen<br>>>> To,<br>>>> David van der Spoel<br>>>><br>>>> Dear Sir,<br>>>><br>>>> I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a<br>
>>> problem.<br>>>> I am giving job for 500000 steps step size 0.002ps (total 1ns) but my<br>>>> job is stopped after 470000 steps. when i run this on 4 processors.<br>>>><br>>>> But the same job is completed on 2 processors.Why this happing i am not<br>
>>> able to understand.<br>>>><br>>>> Another thing is that job for 1500000 steps step size 0.002ps (total<br>>>> 3ns) is stopped after 375000 steps on 2 processors<br>>>> and after 587000 steps on 4 processors, without any error message.<br>
>>><br>>>> What could be the problem and how to solve it, please help me.<br>>>><br>>>> even i tried the 2 same jobs for 1000000 steps step size 0.002ps (total<br>>>> 2ns), one on single processor it is completed in 8 days<br>
>>> but the same job is stop after 550000 steps on 4 processors.<br>>>><br>>>> Is there any change is required in MPI coding or in .mdp files. Sir if<br>>>> you need any other please let me know.<br>
>>><br>>>> Please solve my problem, I will be highly obliged.<br>>>><br>>>><br>>>> DvdS:<br>>>><br>>>> Please upgrade to a recent version. 3.2.1 is more than five years old.<br>
>>><br>>>><br>>>><br>>>> With warm regards.<br>>>> Shikhar<br>>>><br>>>><br>>>><br>>>> --<br>>>> ------------------------------------------------------------<br>
>>> Shikhar Gupta<br>>>> Senior Research Fellow<br>>>> Pharmacoinformatics Department<br>>>> Block- A (Room No.- 208)<br>>>> National Institute of Pharmaceutical Education & Research( NIPER )<br>
>>> Sec- 67, S.A.S Nagar<br>>>> Mohali, Punjab (India)<br>>>> Web-Site: <a href="http://www.niper.ac.in/" target="_blank">www.niper.ac.in</a> <<a href="http://www.niper.ac.in/" target="_blank">http://www.niper.ac.in</a>><br>
>>> PIN- 160062<br>>>> <a href="mailto:Email%3Ashik_sun@rediffmail.com">Email:shik_sun@rediffmail.com</a><br>>>> <mailto:<a href="mailto:Email%253Ashik_sun@rediffmail.com">Email%3Ashik_sun@rediffmail.com</a>>,<a href="mailto:shiksun@gmail.com">shiksun@gmail.com</a><br>
>>> <mailto:<a href="mailto:shiksun@gmail.com">shiksun@gmail.com</a>><br>>>><br>>>><br>>>><br>>>><br>>>> --<br>>>> ------------------------------------------------------------<br>
>>> Shikhar Gupta<br>>>> Senior Research Fellow<br>>>> Pharmacoinformatics Department<br>>>> Block- A (Room No.- 208)<br>>>> National Institute of Pharmaceutical Education & Research( NIPER )<br>
>>> Sec- 67, S.A.S Nagar<br>>>> Mohali, Punjab (India)<br>>>> Web-Site: <a href="http://www.niper.ac.in/" target="_blank">www.niper.ac.in</a> <<a href="http://www.niper.ac.in/" target="_blank">http://www.niper.ac.in</a>><br>
>>> PIN- 160062<br>>>> <a href="mailto:Email%3Ashik_sun@rediffmail.com">Email:shik_sun@rediffmail.com</a><br>>>> <mailto:<a href="mailto:Email%253Ashik_sun@rediffmail.com">Email%3Ashik_sun@rediffmail.com</a>>,<a href="mailto:shiksun@gmail.com">shiksun@gmail.com</a><br>
>>> <mailto:<a href="mailto:shiksun@gmail.com">shiksun@gmail.com</a>><br>>>><br>>>><br>>>> --<br>>>> David van der Spoel, Ph.D., Professor of Biology<br>>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala<br>
>>> 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>>>> 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 <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>>>> 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>>> _______________________________________________<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 <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>>> 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>> ========================================<br>><br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<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>> 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 <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><br><br>------------------------------<br><br>Message: 2<br>
Date: Tue, 25 Aug 2009 00:04:26 +0800<br>From: DreamCatcher <<a href="mailto:huangshuping1987@gmail.com">huangshuping1987@gmail.com</a>><br>Subject: [gmx-users] Something about getting started<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br> <<a href="mailto:4eaf737d0908240904i69e38267mde46802714ce484e@mail.gmail.com">4eaf737d0908240904i69e38267mde46802714ce484e@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br>
<br>Dear gmx-users,<br> I am a freshman of gmx and I wanna use gromacs for polyvinyl-alcohol<br>simulation.But I don't even know how to start it.<br> Is it necessary to start my simulation with a .pdb files?If so,What<br>
should I do before this?I can make an pdb file for a chain of syndiotatic<br>polyvinyl-alcohols via Material Studio or some other packages,but the<br>residue cann't be recognize,so I have to modify some top files to correct<br>
it.I just modify the .hdb and rtp files endeavor to make it.But it seems not<br>an easy work.<br> the message the package sent to me is as follows,appreciate if somebody<br>can help me to handle this!<br>*** (this is an previous version.when i try to use pdb2gmx to get its .top<br>
file,a fatal error reminds:<br> "source code file : resall.c line:279 ()<br> Fatal errors:<br> in .rtp file at line : "<br> when I add the charge and chargegroupndx of the atoms,there comes a<br>
similar error ):<br>My attempt is as follows:<br>### in rtp file<br>[ VAB ]<br> [ atoms ]<br> CB opls_135<br> HB1 opls_140<br> HB2 opls_140<br> HB3 opls_140<br> CA opls_158<br> HA1 opls_140<br> OH opls_154<br> HO opls_155<br>
<br> [ bonds ]<br> CB HB1<br> CB HB2<br> CB HB3<br> CB CA<br> CA HA1<br> CA OH<br> OH HO<br> CA +CB<br><br>[VA ]<br> [ atoms ]<br> CB opls_136<br> HB1 opls_140<br> HB2 opls_140<br> CA opls_158<br>
HA1 opls_140<br> OA opls_154<br> HOA opls_155<br> CG opls_136<br> HG1 opls_140<br> HG2 opls_140<br> CD opls_158<br> HD opls_140<br> OD opls_154<br> HOD opls_155<br><br> [ bonds ]<br> CB -CA<br> CB HB1<br>
CB HB2<br> CB CA<br> CA HA1<br> CA OH<br> OH HO<br> CA CG<br> CG HG1<br> CG HG2<br> CG CD<br> CD HD<br> CD OD<br> OD HOD<br> CD +CB<br><br>[VAE]<br> [ atoms ]<br> CB opls_136<br>
HB1 opls_140<br> HB2 opls_140<br> CA opls_157<br> HA1 opls_140<br> HA2 opls_140<br> OH opls_154<br> HO opls_155<br><br> [ bonds ]<br> CB -CD<br> CB HB1<br> CB HB2<br> CB CA<br> CA HA1<br> CA HA2<br>
CA OH<br> OH HO<br><br>#### in .hdb file:<br>; H add type H i j k<br>VAB 3<br>3 4 HB CB CA +CB<br>1 5 HA CA CB +CB<br>1 2 HO OH CA +CB<br>VA 6<br>2 6 HB CB CA -CA<br>1 5 HA CA CB CG<br>1 2 HOA OA CA CG<br>
2 6 HG CG CA CD<br>1 5 HD CD CG +CB<br>1 1 HOD OD CD CG<br>VAE 3<br>2 6 HB CB CA -CD<br>2 6 HA CA CB +CB<br>1 2 HO OH CA +CB<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>
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<br>------------------------------<br><br>Message: 3<br>Date: Mon, 24 Aug 2009 12:41:00 -0400<br>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>Subject: Re: [gmx-users] Something about getting started<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:4A92C29C.4050206@vt.edu">4A92C29C.4050206@vt.edu</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br><br><br>DreamCatcher wrote:<br>> Dear gmx-users,<br>> I am a freshman of gmx and I wanna use gromacs for<br>> polyvinyl-alcohol simulation.But I don't even know how to start it.<br><br>Then start simple with some tutorial material:<br>
<br><a href="http://oldwiki.gromacs.org/index.php/Tutorials" target="_blank">http://oldwiki.gromacs.org/index.php/Tutorials</a><br><br>> Is it necessary to start my simulation with a .pdb files?If<br><br>You need some sort of structure to start with; .pdb files are generally the<br>
starting point.<br><br>> so,What should I do before this?I can make an pdb file for a chain of<br>> syndiotatic polyvinyl-alcohols via Material Studio or some other<br>> packages,but the residue cann't be recognize,so I have to modify some<br>
> top files to correct it.I just modify the .hdb and rtp files endeavor to<br>> make it.But it seems not an easy work.<br><br>Indeed, it is not. I again suggest you start with some basic tutorials with<br>robust systems so you learn the workflow of a Gromacs simulation. Once you've<br>
got a handle on how everything flows, then attempt your system.<br><br>For polymers, you may find this thread useful:<br><br><a href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html" target="_blank">http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html</a><br>
<br>-Justin<br><br>> the message the package sent to me is as follows,appreciate if<br>> somebody can help me to handle this!<br>> *** (this is an previous version.when i try to use pdb2gmx to get its<br>> .top file,a fatal error reminds:<br>
> "source code file : resall.c line:279 ()<br>> Fatal errors:<br>> in .rtp file at line : "<br>> when I add the charge and chargegroupndx of the atoms,there comes a<br>
> similar error ):<br>> My attempt is as follows:<br>> ### in rtp file<br>> [ VAB ]<br>> [ atoms ]<br>> CB opls_135<br>> HB1 opls_140<br>> HB2 opls_140<br>> HB3 opls_140<br>> CA opls_158<br>
> HA1 opls_140<br>> OH opls_154<br>> HO opls_155<br>><br>> [ bonds ]<br>> CB HB1<br>> CB HB2<br>> CB HB3<br>> CB CA<br>> CA HA1<br>> CA OH<br>> OH HO<br>
> CA +CB<br>><br>> [VA ]<br>> [ atoms ]<br>> CB opls_136<br>> HB1 opls_140<br>> HB2 opls_140<br>> CA opls_158<br>> HA1 opls_140<br>> OA opls_154<br>> HOA opls_155<br>
> CG opls_136<br>> HG1 opls_140<br>> HG2 opls_140<br>> CD opls_158<br>> HD opls_140<br>> OD opls_154<br>> HOD opls_155<br>><br>> [ bonds ]<br>> CB -CA<br>> CB HB1<br>
> CB HB2<br>> CB CA<br>> CA HA1<br>> CA OH<br>> OH HO<br>> CA CG<br>> CG HG1<br>> CG HG2<br>> CG CD<br>> CD HD<br>> CD OD<br>> OD HOD<br>
> CD +CB<br>><br>> [VAE]<br>> [ atoms ]<br>> CB opls_136<br>> HB1 opls_140<br>> HB2 opls_140<br>> CA opls_157<br>> HA1 opls_140<br>> HA2 opls_140<br>> OH opls_154<br>
> HO opls_155<br>><br>> [ bonds ]<br>> CB -CD<br>> CB HB1<br>> CB HB2<br>> CB CA<br>> CA HA1<br>> CA HA2<br>> CA OH<br>> OH HO<br>><br>> #### in .hdb file:<br>
> ; H add type H i j k<br>> VAB 3<br>> 3 4 HB CB CA +CB<br>> 1 5 HA CA CB +CB<br>> 1 2 HO OH CA +CB<br>> VA 6<br>> 2 6 HB CB CA -CA<br>> 1 5 HA CA CB CG<br>> 1 2 HOA OA CA CG<br>
> 2 6 HG CG CA CD<br>> 1 5 HD CD CG +CB<br>> 1 1 HOD OD CD CG<br>> VAE 3<br>> 2 6 HB CB CA -CD<br>> 2 6 HA CA CB +CB<br>> 1 2 HO OH CA +CB<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://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.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><br>Justin A. Lemkul<br>
Ph.D. Candidate<br>ICTAS Doctoral Scholar<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: 4<br>Date: Mon, 24 Aug 2009 14:57:39 -0400<br>From: Jamie Seyed <<a href="mailto:jamie.seyed@gmail.com">jamie.seyed@gmail.com</a>><br>
Subject: Re: [gmx-users] correlation function<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:<br> <<a href="mailto:a9e5cd7b0908241157l69130530j6cfaf4e896ef0da4@mail.gmail.com">a9e5cd7b0908241157l69130530j6cfaf4e896ef0da4@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br>
<br>On Sun, Aug 23, 2009 at 7:32 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br><br>><br>><br>><br>> Actually when I open autocorr.xvg I can see from data/feature<br>
>> extraction/ the last set is S1295 (N=101, autocorr.xvg) which means<br>>> they are 1296 graphs each with poor statistics start at 1 and coming<br>>> down. To have a ACF for a system I expect to get one graph with good<br>
>> statistic... I hope I make it clear now.<br>>><br>><br>> What did you extract with g_traj? All the coordinates of all the<br>> molecules? The command line you gave would be helpful here. It would seem<br>
> that 1296/216 = 6, therefore (and this is just a guess) then g_analyze is<br>> trying to calculate some sort of ACF between all coordinates: x-x, y-y, z-z,<br>> x-y, x-z, y-z. That way, you'd be getting these ACF's for each individual<br>
> molecule. Again, just a guess.<br><br><br>Hi Justin,<br>I think that I extract only the coordinates for my desired atoms using this<br>command:<br>g_traj -f f.xtc -s f.tpr -n f.ndx -ox coord.xvg<br>and then<br>
g_analyze -f coord.xvg -ac autocorr.xvg<br><br>Is that the way to get ACF or I am doing something wrong here?? Many Thanks<br>in Advance/Jamie<br><br><br>><br>><br>> -Justin<br>><br>> --<br>> ========================================<br>
><br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<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>
> 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 <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 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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
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