Re: [gmx-users] Peptide aggregation
Dear Leon, Note that you can already use g_clustsize to check the aggregates. I'll contact you off list next week with the modified version. Ran On Fri, 19 Sep 2008 17:13:02 +0100 Léon Salgado <[EMAIL PROTECTED]> wrote: Dear Dr. Ran Friedman Would you please be so kind to send me your version, to calculate then the rgyr "of the largest aggregate". The box was built with a layer of 1.2 nm around the solute (editconf -d 1.2). Leon Ran Friedman wrote: Dear Leon, You can try to use g_clustsize to get the aggregates. I have a version that can calculate the gyration radius of the largest aggregate, but this would work only if your box is big enough and I haven't tried it with rhombic dodecahedron boxes. Ran. Léon Salgado wrote: Dear gmx users I did some simulations of multimers (peptides) in rhombic dodecahedron boxes. In the initial configuration of the system, the peptides are close of each other in the center of the box. My aim to see if the peptides do aggregate during the trajectory or if they tend to stay apart. A rough estimate can be taken from the gyration radius for all the peptides together. Already did a trjconv -pbc nojump pre-treatment on the trajectory, before calculating the Rgyr. The gyration.xvg plots sometimes do show abrupt jumps, and this is surely due to boundary effects, if I correctly understood the PBC idea. If a peptide approaches the boundary, it appears on the opposite side, thus rgyr will show a false sudden increase. In fact, the peptide could be closer to the rest of the other peptide molecule(s). Thus my question is: how to deal with peptide clusters that span over the periodic boundaries? A similar question was done by Singh: http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html and it was suggested by Chris Neale to pre-process the trajectory (see http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) with: trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump but I'm getting infinite loops on the -pbc cluster treatment, same as reported by Chris (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html). Best, Léon ___ 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 ___ 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 -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Skype: ran.friedman -- ___ 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] Peptide aggregation
Dear Dr. Ran Friedman Would you please be so kind to send me your version, to calculate then the rgyr "of the largest aggregate". The box was built with a layer of 1.2 nm around the solute (editconf -d 1.2). Leon Ran Friedman wrote: Dear Leon, You can try to use g_clustsize to get the aggregates. I have a version that can calculate the gyration radius of the largest aggregate, but this would work only if your box is big enough and I haven't tried it with rhombic dodecahedron boxes. Ran. Léon Salgado wrote: Dear gmx users I did some simulations of multimers (peptides) in rhombic dodecahedron boxes. In the initial configuration of the system, the peptides are close of each other in the center of the box. My aim to see if the peptides do aggregate during the trajectory or if they tend to stay apart. A rough estimate can be taken from the gyration radius for all the peptides together. Already did a trjconv -pbc nojump pre-treatment on the trajectory, before calculating the Rgyr. The gyration.xvg plots sometimes do show abrupt jumps, and this is surely due to boundary effects, if I correctly understood the PBC idea. If a peptide approaches the boundary, it appears on the opposite side, thus rgyr will show a false sudden increase. In fact, the peptide could be closer to the rest of the other peptide molecule(s). Thus my question is: how to deal with peptide clusters that span over the periodic boundaries? A similar question was done by Singh: http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html and it was suggested by Chris Neale to pre-process the trajectory (see http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) with: trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump but I'm getting infinite loops on the -pbc cluster treatment, same as reported by Chris (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html). Best, Léon ___ 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 ___ 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] Peptide aggregation
Dear Leon, You can try to use g_clustsize to get the aggregates. I have a version that can calculate the gyration radius of the largest aggregate, but this would work only if your box is big enough and I haven't tried it with rhombic dodecahedron boxes. Ran. Léon Salgado wrote: > Dear gmx users > > I did some simulations of multimers (peptides) in rhombic dodecahedron > boxes. In the initial configuration of the system, the peptides are > close of each other in the center of the box. > > My aim to see if the peptides do aggregate during the trajectory or if > they tend to stay apart. A rough estimate can be taken from the > gyration radius for all the peptides together. > > Already did a trjconv -pbc nojump pre-treatment on the trajectory, > before calculating the Rgyr. The gyration.xvg plots sometimes do show > abrupt jumps, and this is surely due to boundary effects, if I > correctly understood the PBC idea. If a peptide approaches the > boundary, it appears on the opposite side, thus rgyr will show a false > sudden increase. In fact, the peptide could be closer to the rest of > the other peptide molecule(s). > > Thus my question is: > how to deal with peptide clusters that span over the periodic boundaries? > > A similar question was done by Singh: > http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html > > and it was suggested by Chris Neale to pre-process the trajectory > (see > http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) > with: > > trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster > grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr > trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump > > but I'm getting infinite loops on the -pbc cluster treatment, same as > reported by Chris > (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html). > > Best, > Léon > > ___ > 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 > -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ 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
[gmx-users] Peptide aggregation
Dear gmx users I did some simulations of multimers (peptides) in rhombic dodecahedron boxes. In the initial configuration of the system, the peptides are close of each other in the center of the box. My aim to see if the peptides do aggregate during the trajectory or if they tend to stay apart. A rough estimate can be taken from the gyration radius for all the peptides together. Already did a trjconv -pbc nojump pre-treatment on the trajectory, before calculating the Rgyr. The gyration.xvg plots sometimes do show abrupt jumps, and this is surely due to boundary effects, if I correctly understood the PBC idea. If a peptide approaches the boundary, it appears on the opposite side, thus rgyr will show a false sudden increase. In fact, the peptide could be closer to the rest of the other peptide molecule(s). Thus my question is: how to deal with peptide clusters that span over the periodic boundaries? A similar question was done by Singh: http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html and it was suggested by Chris Neale to pre-process the trajectory (see http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) with: trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump but I'm getting infinite loops on the -pbc cluster treatment, same as reported by Chris (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html). Best, Léon ___ 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
