<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div><blockquote type="cite">I did remove the center of mass motion from my system. But did not do it separately for the lipids and solvent. Oh dear ... thats not good ... is it ? <br></blockquote>Then you should use g_traj to plot the COM of your bilayer and of the water separately and look at them ... <br><blockquote type="cite">Is this just a problem which can be corrected after the simulation, or are the simulations now completely useless ?<br></blockquote>Unfortunately, no! but you do Martini ... rerunning should not be too long? <br><blockquote type="cite">-MAria<br><br><div class="gmail_quote">On Fri, Jul 3, 2009 at 12:27 PM, <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="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://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.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. Re: protein covalently bond to ligand (Tsjerk Wassenaar)<br> 2. waters in ion channels (Samik Bhattacharya)<br> 3. Re: waters in ion channels (Itamar Kass)<br> 4. Re: how to center a MARTINI trajectory so that the lipid<br> bilayer remains at the center of the box (XAvier Periole)<br> (maria goranovic)<br> 5. Re: Re: how to center a MARTINI trajectory so that the lipid<br> bilayer remains at the center of the box (XAvier Periole)<br> (XAvier Periole)<br> <br> <br> ----------------------------------------------------------------------<br> <br> Message: 1<br> Date: Fri, 3 Jul 2009 12:03:48 +0200<br> From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br> Subject: Re: [gmx-users] protein covalently bond to ligand<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID:<br> <<a href="mailto:8ff898150907030303m6d941470j4317dabe6b8935a0@mail.gmail.com">8ff898150907030303m6d941470j4317dabe6b8935a0@mail.gmail.com</a>><br> Content-Type: text/plain; charset=ISO-8859-1<br> <br> Hi <a href="mailto:hazizian@razi.tums.ac.ir">hazizian@razi.tums.ac.ir</a>,<br> <br> I think it's better to only use PRODRG for the pyridoxal phosphate<br> part. Then you can process the rest of the protein as usual,<br> preserving the parameters for lysine backbone and side chain. The PLP<br> part you can renumber and merge with the protein topology, adding<br> bond, angles and dihedrals for the connection. Alternatively you could<br> rewrite the PLP topology as a .rtp entry and add the connection in the<br> file specbond.dat.<br> <br> Hope it helps,<br> <br> Tsjerk<br> <br> On Fri, Jul 3, 2009 at 9:03 AM, hazizian<<a href="mailto:hazizian@razi.tums.ac.ir">hazizian@razi.tums.ac.ir</a>> wrote:<br> > Hi<br> > I want to do MD with a protien with prydoxal phosphate(PLP) which attache<br> > covalently to one lysine.<br> > For this I extract the Toplogy of lysine-PLP from PRODRG server.(DRGGMX.ITP<br> > and DRGPOH.PDB).I Changed the name DRGGMX.ITP to DRG.itp.<br> > after donig<br> > pdb2gmx -f m.pdb -o m1.pdb -water spce with the protein without PLP<br> > (m.pdb=protein whitout covalent bond) , I modified the topol.top file<br> > followig this:<br> > 1- add "DRG.itp" under the forcefield section on topol.top<br> > 2- add "DRG 1" under the molecule sectin of topol.top<br> > also I modifed m1.pdb:<br> > cut the related lysine (LYS 360) in the m1.pdb and paste the modified lysine-<br> > PLP (DRG 360)coordination from DRGPH.PDB.<br> > then I do editconf -f m1.pdb and genbox -f m1.pdb successfully, but when I<br> > want to do grompp the following fatal error appeared:<br> > There is no DRG moleculetype.<br> > what should I do now?<br> > Thanks.<br> > --<br> > Tehran University of Medical Sciences<br> > <a href="http://www.tums.ac.ir" target="_blank">www.tums.ac.ir</a><br> ><br> ><br> > --<br> > This message has been scanned for viruses and<br> > dangerous content by MailScanner, and is<br> > believed to be clean.<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> Tsjerk A. Wassenaar, Ph.D.<br> Junior UD (post-doc)<br> Biomolecular NMR, Bijvoet Center<br> Utrecht University<br> Padualaan 8<br> 3584 CH Utrecht<br> The Netherlands<br> P: +31-30-2539931<br> F: +31-30-2537623<br> <br> <br> ------------------------------<br> <br> Message: 2<br> Date: Fri, 3 Jul 2009 15:38:42 +0530 (IST)<br> From: Samik Bhattacharya <<a href="mailto:samikbhat@yahoo.co.in">samikbhat@yahoo.co.in</a>><br> Subject: [gmx-users] waters in ion channels<br> To: Gromacs <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID: <<a href="mailto:920957.8244.qm@web95412.mail.in2.yahoo.com">920957.8244.qm@web95412.mail.in2.yahoo.com</a>><br> Content-Type: text/plain; charset="iso-8859-1"<br> <br> hi i'm simulating a ion channel protein in DPPC membrane. i'm following Justin's tutorial for that. and have completed upto the solvation step. but right after solvation, i found some water molecules in the channel. now i want to delete those molecules. in the tutorial it is advised tyo use the keepbyz script to do that.. but after using that i didn't find any change in the structure. watres are still present in there. may be i am making some mistake in running the program or something like that!!! can anyone suggest any thing to solve the problem...thanking you all in advance.<br> <br> <br> <br> Looking for local information? Find it on Yahoo! Local <a href="http://in.local.yahoo.com/" target="_blank">http://in.local.yahoo.com/</a><br> -------------- next part --------------<br> An HTML attachment was scrubbed...<br> URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/266f5139/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/266f5139/attachment-0001.html</a><br> <br> ------------------------------<br> <br> Message: 3<br> Date: Fri, 3 Jul 2009 20:12:37 +1000<br> From: Itamar Kass <<a href="mailto:itamar.kass@gmail.com">itamar.kass@gmail.com</a>><br> Subject: Re: [gmx-users] waters in ion channels<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID:<br> <<a href="mailto:c0962a4d0907030312x4b947700l66e349598d2009dd@mail.gmail.com">c0962a4d0907030312x4b947700l66e349598d2009dd@mail.gmail.com</a>><br> Content-Type: text/plain; charset=ISO-8859-1<br> <br> Hi,<br> <br> I would say that those are water molecule which enter from the bulk<br> water. This is normal and probably important for the physiological<br> function of the system.<br> <br> Best,<br> Itamar<br> <br> On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharya<<a href="mailto:samikbhat@yahoo.co.in">samikbhat@yahoo.co.in</a>> wrote:<br> > hi i'm simulating a ion channel protein in DPPC membrane. i'm following<br> > Justin's tutorial for that. and have completed upto the solvation step. but<br> > right after solvation, i found some water molecules in the channel. now i<br> > want to delete those molecules. in the tutorial it is advised tyo use the<br> > keepbyz script to do that.. but after using that i didn't find any change<br> > in the structure. watres are still present in there. may be i am making some<br> > mistake in running the program or something like that!!! can anyone suggest<br> > any thing to solve the problem...thanking you all in advance.<br> ><br> > ________________________________<br> > Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8.<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> Message: 4<br> Date: Fri, 3 Jul 2009 12:19:48 +0200<br> From: maria goranovic <<a href="mailto:mariagoranovic@gmail.com">mariagoranovic@gmail.com</a>><br> Subject: [gmx-users] Re: how to center a MARTINI trajectory so that<br> the lipid bilayer remains at the center of the box (XAvier Periole)<br> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> Message-ID:<br> <<a href="mailto:9024f1330907030319y77bc41e3wd3b4618959780b1b@mail.gmail.com">9024f1330907030319y77bc41e3wd3b4618959780b1b@mail.gmail.com</a>><br> Content-Type: text/plain; charset="iso-8859-1"<br> <br> Well the bilayer drifts down in the z-direction, and eventually the leaflets<br> almost separate, with each leaflet being on opposite ends of the box.<br> <br> if i try pbc nojump, the lipids drift far away from the box in the xy plane<br> <br> On Fri, Jul 3, 2009 at 12:00 PM, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<br> <br> > 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://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.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. Re: how to center a MARTINI trajectory so that the lipid<br> > bilayer remains at the center of the box (XAvier Periole)<br> ><br> ><br> > ----------------------------------------------------------------------<br> ><br> > Message: 1<br> > Date: Fri, 3 Jul 2009 11:43:55 +0200<br> > From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br> > Subject: Re: [gmx-users] how to center a MARTINI trajectory so that<br> > the lipid bilayer remains at the center of the box<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:EEA7DAA1-6584-4AF0-8321-3FEA30A413F4@rug.nl">EEA7DAA1-6584-4AF0-8321-3FEA30A413F4@rug.nl</a>><br> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br> ><br> ><br> > What is the problem exactly? The two layers separate over the pbc?<br> > did you try a -pbc nojump prior the centering?<br> ><br> > On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:<br> ><br> > > Dear All,<br> > ><br> > > This has been discussed before for individual frames. But I am<br> > > having a problem in trying to center a trajectory so that the<br> > > bilayer remains at the center of the box. I have tried several<br> > > combinations, but none of the them work. In each case, the centering<br> > > and/or the fitting is done on the lipid bilayer itself.<br> > ><br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > center -boxcenter zero -pbc mol<br> > ><br> > > this one works for one particular .gro file, but not for the whole<br> > > trajectory. I tried all of the following, but none of them work.<br> > > What is the solution ?<br> > ><br> > ><br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > center -boxcenter zero<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc<br> > > mol -boxcenter zero<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc<br> > > mol -center<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > pbc mol -fit trans<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > pbc mol -fit trans -center<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > pbc mol -fit trans -center -boxcenter zero<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit<br> > > trans<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit<br> > > progressive<br> > ><br> > > --<br> > > Maria G.<br> > > Technical University of Denmark<br> > > Copenhagen<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> > _______________________________________________<br> > gmx-users mailing list<br> > <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> ><br> > End of gmx-users Digest, Vol 63, Issue 11<br> > *****************************************<br> ><br> <br> <br> <br> --<br> Maria G.<br> Technical University of Denmark<br> Copenhagen<br> -------------- next part --------------<br> An HTML attachment was scrubbed...<br> URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/e16931da/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/e16931da/attachment-0001.html</a><br> <br> ------------------------------<br> <br> Message: 5<br> Date: Fri, 3 Jul 2009 12:26:43 +0200<br> From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br> Subject: Re: [gmx-users] Re: how to center a MARTINI trajectory so<br> that the lipid bilayer remains at the center of the box (XAvier<br> Periole)<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:1D610226-9AC2-419C-8233-633D4F1F1BEA@rug.nl">1D610226-9AC2-419C-8233-633D4F1F1BEA@rug.nl</a>><br> Content-Type: text/plain; charset="us-ascii"<br> <br> <br> This sounds pretty bad! You have a drift of your all system<br> apparently ...<br> Did you not remove the COM of your system?<br> For membranes it is often recommended to remove the water and the<br> lipid bilayer separately. The might drift one from the other.<br> <br> On Jul 3, 2009, at 12:19 PM, maria goranovic wrote:<br> <br> > Well the bilayer drifts down in the z-direction, and eventually the<br> > leaflets almost separate, with each leaflet being on opposite ends<br> > of the box.<br> ><br> > if i try pbc nojump, the lipids drift far away from the box in the<br> > xy plane<br> ><br> > On Fri, Jul 3, 2009 at 12:00 PM, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>><br> > wrote:<br> > 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://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.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. Re: how to center a MARTINI trajectory so that the lipid<br> > bilayer remains at the center of the box (XAvier Periole)<br> ><br> ><br> > ----------------------------------------------------------------------<br> ><br> > Message: 1<br> > Date: Fri, 3 Jul 2009 11:43:55 +0200<br> > From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br> > Subject: Re: [gmx-users] how to center a MARTINI trajectory so that<br> > the lipid bilayer remains at the center of the box<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:EEA7DAA1-6584-4AF0-8321-3FEA30A413F4@rug.nl">EEA7DAA1-6584-4AF0-8321-3FEA30A413F4@rug.nl</a>><br> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br> ><br> ><br> > What is the problem exactly? The two layers separate over the pbc?<br> > did you try a -pbc nojump prior the centering?<br> ><br> > On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:<br> ><br> > > Dear All,<br> > ><br> > > This has been discussed before for individual frames. But I am<br> > > having a problem in trying to center a trajectory so that the<br> > > bilayer remains at the center of the box. I have tried several<br> > > combinations, but none of the them work. In each case, the centering<br> > > and/or the fitting is done on the lipid bilayer itself.<br> > ><br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > center -boxcenter zero -pbc mol<br> > ><br> > > this one works for one particular .gro file, but not for the whole<br> > > trajectory. I tried all of the following, but none of them work.<br> > > What is the solution ?<br> > ><br> > ><br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > center -boxcenter zero<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc<br> > > mol -boxcenter zero<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc<br> > > mol -center<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > pbc mol -fit trans<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > pbc mol -fit trans -center<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > > pbc mol -fit trans -center -boxcenter zero<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit<br> > > trans<br> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit<br> > > progressive<br> > ><br> > > --<br> > > Maria G.<br> > > Technical University of Denmark<br> > > Copenhagen<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> > _______________________________________________<br> > gmx-users mailing list<br> > <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> ><br> > End of gmx-users Digest, Vol 63, Issue 11<br> > *****************************************<br> ><br> ><br> ><br> > --<br> > Maria G.<br> > Technical University of Denmark<br> > Copenhagen<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> -------------- next part --------------<br> An HTML attachment was scrubbed...<br> URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/1aec8a26/attachment.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/1aec8a26/attachment.html</a><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://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> <br> End of gmx-users Digest, Vol 63, Issue 12<br> *****************************************<br> </blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></body></html>