Re: [gmx-users] Imaging in PBC simulations -summary
Dear Jochen and Tamas, thanks for your replies. I tried both, the trjconv -fit postprocessing and setting comm_mode for mdrun and actually only the latter worked fine. In the former, protein drifts toward the box side and jumps out for some frames, leaving its bound ions inside the box. Better to remove translation during the run. All the best, Martin Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and not set. I watch the movie in VMD, loading first a starting gro and than the trr. The problem is that the protein creeps out of the box (the same happens when using ngmx). I have tried various variants of post-processing using trjconv -fit (translation) -pbc (inbox, whole) -center (tric), groups for fitting: protein or system. But in any case, the result is the same. Could you please advice me how to solve this? Whether it is better to include some parameter for mdrun or to post-process in a different way? Looking forward to hearing from you. Yours sincerely, Martin Lepsik You can either use comm_grps = Protein and comm_mode = Linear or use trjconv with the -fit option and fit your protein on the starting position after finishing the simulation. Cheers, Jochen -- -- Martin Lepsik, Ph.D. Laboratoire de Dynamique Moléculaire (LDM) Institut de Biologie Structurale 41, rue Jules Horowitz 38027 Grenoble Cedex 1, France tel: +33-4-3878-4780 e-mail: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Imaging in PBC simulations
Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD, loading first a starting gro and than the trr. The problem is that the protein creeps out of the box (the same happens when using ngmx). I have tried various variants of post-processing using trjconv -fit (translation) -pbc (inbox, whole) -center (tric), groups for fitting: protein or system. But in any case, the result is the same. Could you please advice me how to solve this? Whether it is better to include some parameter for mdrun or to post-process in a different way? Looking forward to hearing from you. Yours sincerely, Martin Lepsik -- -- Martin Lepsik, Ph.D. Laboratoire de Dynamique Moléculaire (LDM) Institut de Biologie Structurale 41, rue Jules Horowitz 38027 Grenoble Cedex 1, France tel: +33-4-3878-4780 e-mail: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Imaging in PBC simulations
I wrote a program using bioJava, that recenters the protein in every frame... that does the job quite nicely, but there maybe other options.On 4/24/06, Martin LEPSIK [EMAIL PROTECTED] wrote:Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best wayto image a protein with a ligand insidea triclinic water box?I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD,loading first a starting gro and than the trr. The problem is that theprotein creeps out of the box (the same happenswhen using ngmx).I have tried various variants of post-processing using trjconv -fit (translation) -pbc (inbox, whole) -center (tric),groups for fitting: protein or system. But in any case, the result isthe same.Could you please advice me how to solve this? Whether it is better toinclude some parameter for mdrun or to post-process in a different way?Looking forward to hearing from you.Yours sincerely,Martin LepsikMartin Lepsik, Ph.D.Laboratoire de Dynamique Moléculaire (LDM) Institut de Biologie Structurale41, rue Jules Horowitz38027 Grenoble Cedex 1, Francetel: +33-4-3878-4780e-mail: [EMAIL PROTECTED]___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 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] Imaging in PBC simulations
Martin LEPSIK wrote: Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD, loading first a starting gro and than the trr. The problem is that the protein creeps out of the box (the same happens when using ngmx). I have tried various variants of post-processing using trjconv -fit (translation) -pbc (inbox, whole) -center (tric), groups for fitting: protein or system. But in any case, the result is the same. Could you please advice me how to solve this? Whether it is better to include some parameter for mdrun or to post-process in a different way? Looking forward to hearing from you. Yours sincerely, Martin Lepsik You can either use comm_grps = Protein and comm_mode = Linear or use trjconv with the -fit option and fit your protein on the starting position after finishing the simulation. Cheers, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Imaging in PBC simulations
Martin LEPSIK wrote: Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD, loading first a starting gro and than the trr. The problem is that the protein creeps out of the box (the same happens when using ngmx). I have tried various variants of post-processing using trjconv -fit (translation) -pbc (inbox, whole) -center (tric), groups for fitting: protein or system. But in any case, the result is the same. Could you please advice me how to solve this? Whether it is better to include some parameter for mdrun or to post-process in a different way? Looking forward to hearing from you. Yours sincerely, Martin Lepsik You can either use comm_grps = Protein and comm_mode = Linear or use trjconv with the -fit option and fit your protein on the starting position after finishing the simulation. Cheers, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
