Re: [gmx-users] trjconv -pbc: how to keep all parts of the system clustered together in PDB?
I thought I was sure -pbc cluster will work, but it doesn't :( trjconv get's stuck on an infinite loop while calculating center of mass. In an index.ndx I created a new group which I called CLUSTER, as Mark suggested (I used make_ndx), then I ran trjconv: trjconv -f 1Y2Elig_em.trr -s 1Y2Elig_em.tpr -o tmp.pdb -b 120 -e 125 -pbc cluster -n index.ndx What I get is an infinite loop: COM:2.784 1.968 3.409 iter = 1 Isq = 1840514.500 COM:4.175 5.905 3.409 iter = 2 Isq = 230100.828 COM:2.784 1.968 3.409 iter = 3 Isq = 1840514.500 COM:4.175 5.905 3.409 iter = 4 Isq = 230100.828 COM:2.784 1.968 3.409 iter = 5 Isq = 1840514.500 COM:4.175 5.905 3.409 iter = 6 Isq = 230100.828 COM:2.784 1.968 3.409 iter = 7 Isq = 1840514.500 COM:4.175 5.905 3.409 iter = 8 Isq = 230100.828 COM:2.784 1.968 3.409 iter = 9 Isq = 1840514.500 COM:4.175 5.905 3.409 iter = 10 Isq = 230100.828 ... which goes on forever... What am I doing wrong? (Should I attach the files?) Thank you for your time! Vis Dear GROMACS users and gurus, I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been driving me crazy. I have a protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces clustered compactly for some postprocessing, using trjconv for conversion of trr/xtc into PDB format: -pbc mol option of trjconv: metal ions are far from the rest of the protein. -pbc nojump or -pbc whole: inhibitor far from the protein, metals are fine. -pbc atom or -pbc res: couple of residues are disattached from the protein; metals and inhibitor are fine. -pbc cluster: doesn't work (irrelevant?) -pbc cluster should work with a suitable index group of protein+metal+inhibitor - that's what it is for. Once that's done, you may want to re-run trjconv to apply other effects. Two-pass processing is often necessary. Also -center and -boxcenter don't seem to help... Can anybody suggest some tricks? I used octahedral box for my runs. don't seem to help also doesn't help. We can't guess what it was about your inputs and outputs that was contrary to your hopes :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv -pbc: how to keep all parts of the system clustered together in PDB?
Thank you, Mark, for your tip, the indexing solution is perfect! Regards, Vis --- On Tue, 12/22/09, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] trjconv -pbc: how to keep all parts of the system clustered together in PDB? To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, December 22, 2009, 7:29 PM Visvaldas K. wrote: Dear GROMACS users and gurus, I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been driving me crazy. I have a protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces clustered compactly for some postprocessing, using trjconv for conversion of trr/xtc into PDB format: -pbc mol option of trjconv: metal ions are far from the rest of the protein. -pbc nojump or -pbc whole: inhibitor far from the protein, metals are fine. -pbc atom or -pbc res: couple of residues are disattached from the protein; metals and inhibitor are fine. -pbc cluster: doesn't work (irrelevant?) -pbc cluster should work with a suitable index group of protein+metal+inhibitor - that's what it is for. Once that's done, you may want to re-run trjconv to apply other effects. Two-pass processing is often necessary. Also -center and -boxcenter don't seem to help... Can anybody suggest some tricks? I used octahedral box for my runs. don't seem to help also doesn't help. We can't guess what it was about your inputs and outputs that was contrary to your hopes :-) Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trjconv -pbc: how to keep all parts of the system clustered together in PDB?
Dear GROMACS users and gurus, I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been driving me crazy. I have a protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces clustered compactly for some postprocessing, using trjconv for conversion of trr/xtc into PDB format: -pbc mol option of trjconv: metal ions are far from the rest of the protein. -pbc nojump or -pbc whole: inhibitor far from the protein, metals are fine. -pbc atom or -pbc res: couple of residues are disattached from the protein; metals and inhibitor are fine. -pbc cluster: doesn't work (irrelevant?) Also -center and -boxcenter don't seem to help... Can anybody suggest some tricks? I used octahedral box for my runs. Sincerely, Vis Kairys -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
