Are you sure you are actually doing minimization and not MD? Check the integrator option in the mdp file. Also take a look at: <br><a href="http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings">http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings</a><br>
<br>Roland<br><br><div class="gmail_quote">On Tue, Mar 3, 2009 at 6:19 AM, <span dir="ltr"><<a href="mailto:mhviet@ifpan.edu.pl">mhviet@ifpan.edu.pl</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thank David very much<br>
I have tried and most of them work.<br>
And, When I run script_mini.mdp to minimize energy and it report LINCS<br>
warning (as below). So Can you tell me What LINCS WARNING mean?<br>
<br>
Step 16, time 0.032 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.000000, max 0.000001 (between atoms 18 and 20)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
97 98 35.3 0.1000 0.1000 0.1000<br>
<br>
<br>
<br>
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> 1. Detail of Script.sh in Gromacs-4.0.3? (<a href="mailto:mhviet@ifpan.edu.pl">mhviet@ifpan.edu.pl</a>)<br>
> 2. Re: How to define protein surface residues (David van der Spoel)<br>
> 3. Re: Detail of Script.sh in Gromacs-4.0.3? (David van der Spoel)<br>
> 4. SV: SV: [gmx-users] g_order version 4.0.x (Sarah Witzke)<br>
><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Tue, 3 Mar 2009 10:37:05 +0100 (CET)<br>
> From: <a href="mailto:mhviet@ifpan.edu.pl">mhviet@ifpan.edu.pl</a><br>
> Subject: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?<br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Message-ID:<br>
> <<a href="mailto:24e6018b503b7a1516fccea3477b4d8d.squirrel@webmail.ifpan.edu.pl">24e6018b503b7a1516fccea3477b4d8d.squirrel@webmail.ifpan.edu.pl</a>><br>
> Content-Type: text/plain;charset=iso-8859-1<br>
><br>
> Dear all<br>
><br>
> I am newer in Gromacs. Now I am studying Gomacs for protein simulations. I<br>
> am trying script files which used for gromacs-3. Can I do it? Does<br>
> Gromacs-4. have to use others script files? and If It have, Can you send<br>
> sript files to me for gromacs-4?<br>
> Thank you verry much!<br>
><br>
> Yours truly,<br>
><br>
> Man Hoang Viet<br>
><br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Tue, 03 Mar 2009 10:52:07 +0100<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] How to define protein surface residues<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:49ACFDC7.6060402@xray.bmc.uu.se">49ACFDC7.6060402@xray.bmc.uu.se</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
> Lee Soin wrote:<br>
>> Hello!<br>
>> I'm trying to find the surface residues of a protein. Maybe this should<br>
>> be calculated by myself and not using GROMACS. Can anybody tell me a<br>
>> feasible procedure for doing so? Thanks!<br>
>><br>
> g_sas<br>
><br>
>> --<br>
>> Sun Li<br>
>> Department of Physics<br>
>> Nanjing University, China<br>
>><br>
>><br>
>> ------------------------------------------------------------------------<br>
>><br>
>> _______________________________________________<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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>> Please don't post (un)subscribe requests to the list. Use the<br>
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><br>
><br>
> --<br>
> David van der Spoel, Ph.D., Professor of Biology<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: 3<br>
> Date: Tue, 03 Mar 2009 10:54:42 +0100<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] Detail of Script.sh in Gromacs-4.0.3?<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:49ACFE62.6030603@xray.bmc.uu.se">49ACFE62.6030603@xray.bmc.uu.se</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
> <a href="mailto:mhviet@ifpan.edu.pl">mhviet@ifpan.edu.pl</a> wrote:<br>
>> Dear all<br>
>><br>
>> I am newer in Gromacs. Now I am studying Gomacs for protein simulations.<br>
>> I<br>
>> am trying script files which used for gromacs-3. Can I do it? Does<br>
>> Gromacs-4. have to use others script files? and If It have, Can you send<br>
>> sript files to me for gromacs-4?<br>
>> Thank you verry much!<br>
><br>
> Have you tried?<br>
><br>
> Most of them will work.<br>
><br>
>><br>
>> Yours truly,<br>
>><br>
>> Man Hoang Viet<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<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>
> David van der Spoel, Ph.D., Professor of Biology<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: 4<br>
> Date: Tue, 3 Mar 2009 11:37:56 +0100<br>
> From: "Sarah Witzke" <<a href="mailto:sawit02@student.sdu.dk">sawit02@student.sdu.dk</a>><br>
> Subject: SV: SV: [gmx-users] g_order version 4.0.x<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:3BC166246158F845A8ABBACA9EEE1E2D09147BB0@ADM-EXCH0C.adm.c.sdu.dk">3BC166246158F845A8ABBACA9EEE1E2D09147BB0@ADM-EXCH0C.adm.c.sdu.dk</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> Good idea, I'll try that when I get home next week.<br>
><br>
> -Sarah<br>
><br>
> ________________________________<br>
><br>
> Fra: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> på vegne af Justin A. Lemkul<br>
> Sendt: ma 02-03-2009 13:58<br>
> Til: Discussion list for GROMACS users<br>
> Emne: Re: SV: [gmx-users] g_order version 4.0.x<br>
><br>
><br>
><br>
><br>
><br>
> Sarah Witzke wrote:<br>
>> Thank you David, I have filled a bugzilla.<br>
>><br>
><br>
> g_order works for me under version 4.0.4, perhaps try an upgrade?<br>
><br>
> -Justin<br>
><br>
> ________________________________<br>
>><br>
>> Fra: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> på vegne af David van der Spoel<br>
>> Sendt: ma 02-03-2009 10:55<br>
>> Til: Discussion list for GROMACS users<br>
>> Emne: Re: [gmx-users] g_order version 4.0.x<br>
>><br>
>><br>
>><br>
>> Sarah Witzke wrote:<br>
>>> Dear Gromacs users,<br>
>>><br>
>>><br>
>>><br>
>>> I'm sorry to resend this email but I sent it yesterday (27 hours ago)<br>
>>> and I still haven't received it myself. I'm sorry for the inconvenience<br>
>>> it might cause.<br>
>>><br>
>>><br>
>>><br>
>>> Sarah<br>
>>><br>
>>><br>
>>> ________________________________<br>
>>><br>
>>> Dear Gromacs Users,<br>
>>><br>
>>><br>
>>><br>
>>> I have simulated a lipid bilayer (128 DMPC molecules) with some small<br>
>>> hydrophobic molecules. These small molecules go from the water into the<br>
>>> bilayer and I now want to do some analysis to see, whether this has<br>
>>> changed e.g. membrane thickness or the order of the lipid tails. I'm<br>
>>> new to gromacs and this is my first try with analysis.<br>
>>><br>
>>> For analysing the order of the lipid tales, I use g_order. The first<br>
>>> index file I created consisted of 28 groups - one for each of the 14<br>
>>> carbons (including the carbonyl-C) in the two chains. The atoms in each<br>
>>> of the 128 lipid molecules have the same atom name (e.g. c1, c2...) so<br>
>>> each of the 28 groups in the index file consist of 128 atoms (an entry<br>
>>> in make_ndx would look like this "a c15 & r DMPC").<br>
>>><br>
>>> Then I tried g_order version 4.0.2:<br>
>>><br>
>>><br>
>>><br>
>>> g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b<br>
>>> 100000 -od dmpclim3_order_2.xvg<br>
>>><br>
>>><br>
>>><br>
>>> I'm asked to "Select the group that contains the atoms you want to use<br>
>>> for the tetrahedrality order parameter calculation:" and then all the<br>
>>> 28 groups are listed. This was not what I had expected; I thought<br>
>>> g_order calculated the order parameter for all the tail carbons at<br>
>>> once. I tried just choosing group 0 to see what happened: Not much - as<br>
>>> was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg.<br>
>>> This I found strange since I hadn't asked for them, but then I found<br>
>>> this bugzilla report:<br>
>>> <a href="http://www.gromacs.org/component/option,com_wrapper/Itemid,157/" target="_blank">http://www.gromacs.org/component/option,com_wrapper/Itemid,157/</a><br>
>>> <<a href="https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/" target="_blank">https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/</a>><br>
>>> (no. 264)<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> After reading that I also tried to specify all carbons in one single<br>
>>> group and then run g_order again:<br>
>>><br>
>>><br>
>>><br>
>>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b<br>
>>> 100000 -od dmpclim3_order_2.xvg<br>
>>><br>
>>><br>
>>><br>
>>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)<br>
>>><br>
>>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)<br>
>>><br>
>>> Select the group that contains the atoms you want to use for the<br>
>>> tetrahedrality order parameter calculation:<br>
>>><br>
>>> Group 0<br>
>>> (C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC)<br>
>>> has 3584 elements<br>
>>><br>
>>> There is one group in the index<br>
>>><br>
>>> Reading frame 0 time 100000.008<br>
>>><br>
>>> Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1#<br>
>>><br>
>>><br>
>>><br>
>>> Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1#<br>
>>><br>
>>> Reading frame 11000 time 210000.016<br>
>>><br>
>>><br>
>>><br>
>>> Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted<br>
>>> deuterium order .xvg file.<br>
>>><br>
>>><br>
>>><br>
>>> So, in the bugzilla report it also said that the problem had been fixed<br>
>>> in the CVS. Unfortunately I don't know what this is, could anyone<br>
>>> explain me please?<br>
>>><br>
>>><br>
>>><br>
>>> I tried g_order version 4.0.3 (again with the index file with only one<br>
>>> group):<br>
>>><br>
>>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b<br>
>>> 100000 -od dmpclim3_order_3.xvg<br>
>>><br>
>>><br>
>>><br>
>>> Taking z axis as normal to the membrane<br>
>>><br>
>>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)<br>
>>><br>
>>> Using following groups:<br>
>>><br>
>>> Groupname:<br>
>>> C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC<br>
>>> First atomname: C15 First atomnr 44<br>
>>><br>
>>><br>
>>><br>
>>> Reading frame 0 time 100000.008 Number of elements in first<br>
>>> group: 3584<br>
>>><br>
>>> Reading frame 11000 time 210000.016<br>
>>><br>
>>><br>
>>><br>
>>> Read trajectory. Printing parameters to file<br>
>>><br>
>>><br>
>>><br>
>>> Now two order files are generated: The wanted dmpclim3_order_3.xvg and<br>
>>> also order.xvg which I didn't request for. (No sg-ang.xvg and<br>
>>> sk-dist.xvg this time).<br>
>>><br>
>>> Unfortunately neither of the obtained .xvg files contain any order<br>
>>> parameters:<br>
>>><br>
>>><br>
>>><br>
>>> dmpclim3_order_3.xvg:<br>
>>><br>
>>> # This file was created Sat Feb 28 20:02:09 2009<br>
>>><br>
>>> # by the following command:<br>
>>><br>
>>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b<br>
>>> 100000 -od dmpclim3_order_3.xvg<br>
>>><br>
>>> #<br>
>>><br>
>>> # g_order is part of G R O M A C S:<br>
>>><br>
>>> #<br>
>>><br>
>>> # Great Red Oystrich Makes All Chemists Sane<br>
>>><br>
>>> #<br>
>>><br>
>>> @ title "Deuterium order parameters"<br>
>>><br>
>>> @ xaxis label "Atom"<br>
>>><br>
>>> @ yaxis label "Scd"<br>
>>><br>
>>> @TYPE xy<br>
>>><br>
>>><br>
>>><br>
>>> order.xvg:<br>
>>><br>
>>> # This file was created Sat Feb 28 20:02:09 2009<br>
>>><br>
>>> # by the following command:<br>
>>><br>
>>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b<br>
>>> 100000 -od dmpclim3_order_3.xvg<br>
>>><br>
>>> #<br>
>>><br>
>>> # g_order is part of G R O M A C S:<br>
>>><br>
>>> #<br>
>>><br>
>>> # Great Red Oystrich Makes All Chemists Sane<br>
>>><br>
>>> #<br>
>>><br>
>>> @ title "Order tensor diagonal elements"<br>
>>><br>
>>> @ xaxis label "Atom"<br>
>>><br>
>>> @ yaxis label "S"<br>
>>><br>
>>> @TYPE xy<br>
>>><br>
>>><br>
>>><br>
>>> I will be very thankful if anyone has any suggestions as to what I'm<br>
>>> doing wrong?<br>
>>><br>
>>><br>
>> Please submit a bugzilla.<br>
>> I fixed something before 4.0.3, but apparently not everything.<br>
>><br>
>> --<br>
>> David van der Spoel, Ph.D., Professor of Biology<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>
>> <<a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</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://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<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>
>> 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<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>
> Graduate Research Assistant<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>
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</blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>