Re: [gmx-users] How to center my trimer in my simulation box.
On Tue, 22 Apr 2008 14:14:19 -0700 Ilya Chorny [EMAIL PROTECTED] wrote: Hello, I am simulating a trimer in a membrane. In one of my simulation two of the monomers are on one side of the box and the other monomer is on the other side of the box. I tried using trjconv to center the whole thing in the center of my simulation cell but have failed miserably. I also searched around for about an hour and could not find anything. I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro. first run trjconv -pbc nojump Any advice? Thanks, Ilya -- Ilya Chorny Ph.D. - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to center my trimer in my simulation box.
Just to clarify. I would run trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro? What would I run next? Thanks, Ilya On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Tue, 22 Apr 2008 14:14:19 -0700 Ilya Chorny [EMAIL PROTECTED] wrote: Hello, I am simulating a trimer in a membrane. In one of my simulation two of the monomers are on one side of the box and the other monomer is on the other side of the box. I tried using trjconv to center the whole thing in the center of my simulation cell but have failed miserably. I also searched around for about an hour and could not find anything. I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro. first run trjconv -pbc nojump Any advice? Thanks, Ilya -- Ilya Chorny Ph.D. - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to center my trimer in my simulation box.
So I got it to center my protein (using -pbc nojump) and keep the trimer and the membrane in tact but it completely destroyed my water. I was hoping I could get the whole simulation box back with the protein in the center. Is that possible? Thanks, Ilya On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny [EMAIL PROTECTED] wrote: Just to clarify. I would run trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro? What would I run next? Thanks, Ilya On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Tue, 22 Apr 2008 14:14:19 -0700 Ilya Chorny [EMAIL PROTECTED] wrote: Hello, I am simulating a trimer in a membrane. In one of my simulation two of the monomers are on one side of the box and the other monomer is on the other side of the box. I tried using trjconv to center the whole thing in the center of my simulation cell but have failed miserably. I also searched around for about an hour and could not find anything. I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro. first run trjconv -pbc nojump Any advice? Thanks, Ilya -- Ilya Chorny Ph.D. - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole http://md.chem.rug.nl/%7Eperiole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to center my trimer in my simulation box.
I've often found it necessary to do multiple trjconv steps to get the result I want. So in this case, I'd probably make sure my protein is genuinely centered in the box, then take that output .xtc and then make sure everything is whole and approximately in the box (-pbc whole). - Original Message From: Ilya Chorny [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, April 22, 2008 11:52:23 PM Subject: Re: [gmx-users] How to center my trimer in my simulation box. So I got it to center my protein (using -pbc nojump) and keep the trimer and the membrane in tact but it completely destroyed my water. I was hoping I could get the whole simulation box back with the protein in the center. Is that possible? Thanks, Ilya On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny [EMAIL PROTECTED] wrote: Just to clarify. I would run trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro? What would I run next? Thanks, Ilya On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Tue, 22 Apr 2008 14:14:19 -0700 Ilya Chorny [EMAIL PROTECTED] wrote: Hello, I am simulating a trimer in a membrane. In one of my simulation two of the monomers are on one side of the box and the other monomer is on the other side of the box. I tried using trjconv to center the whole thing in the center of my simulation cell but have failed miserably. I also searched around for about an hour and could not find anything. I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro. first run trjconv -pbc nojump Any advice? Thanks, Ilya -- Ilya Chorny Ph.D. - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D. Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to center my trimer in my simulation box.
So I got it to work for my trimer by doing the following. 1.) trjconv -f *.xtc -s *.tpr -pbc nojump -o out.xtc 2.) trjconv -f out.xtc -s *.tpr -pbc mol -center -boxcenter rect The first step unwraps the whole trajectory and the second step wraps it back up. Cheers, Ilya -- Ilya Chorny Ph.D. On Tue, Apr 22, 2008 at 4:30 PM, Alan Dodd [EMAIL PROTECTED] wrote: I've often found it necessary to do multiple trjconv steps to get the result I want. So in this case, I'd probably make sure my protein is genuinely centered in the box, then take that output .xtc and then make sure everything is whole and approximately in the box (-pbc whole). - Original Message From: Ilya Chorny [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, April 22, 2008 11:52:23 PM Subject: Re: [gmx-users] How to center my trimer in my simulation box. So I got it to center my protein (using -pbc nojump) and keep the trimer and the membrane in tact but it completely destroyed my water. I was hoping I could get the whole simulation box back with the protein in the center. Is that possible? Thanks, Ilya On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny [EMAIL PROTECTED] wrote: Just to clarify. I would run trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro? What would I run next? Thanks, Ilya On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Tue, 22 Apr 2008 14:14:19 -0700 Ilya Chorny [EMAIL PROTECTED] wrote: Hello, I am simulating a trimer in a membrane. In one of my simulation two of the monomers are on one side of the box and the other monomer is on the other side of the box. I tried using trjconv to center the whole thing in the center of my simulation cell but have failed miserably. I also searched around for about an hour and could not find anything. I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro. first run trjconv -pbc nojump Any advice? Thanks, Ilya -- Ilya Chorny Ph.D. - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D. -- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
