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><br>Is this just a problem which can be corrected after the simulation, or are the simulations now completely useless ?<br>
<br>-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;">
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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>
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><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>
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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>
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> or, via email, send a message with subject or body 'help' to<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: 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>
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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>
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> > 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>
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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>