Re: [gmx-users] Centering the system
On 10/17/13 2:09 PM, Shima Arasteh wrote: I used -fit or boxcenter or trans or .. any other thing which I though to solve my problem, but did not work. Would you give me a hint pleaaasssee? trjconv -center or trjconv -fit transxy -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Centering the system
I used -fit or boxcenter or trans or .. any other thing which I though to solve my problem, but did not work. Would you give me a hint pleaaasssee? Thanks a lot. Sincerely, Shima On Wednesday, October 16, 2013 4:05 PM, Justin Lemkul wrote: On 10/16/13 8:29 AM, Shima Arasteh wrote: > > > Dear gmx users, > > I have a system consist of a lipid bilayer and a peptide. As the initial > configuration, the peptide is located in center of the x-y plane above lipid > bilayer. After running MD, the peptide shows interactions with the polar > groups. It's ok, but the peptide is near one edge of the x-y plane of the > bilayer. I' d like to know if there is any way to use the properties of the > pbc and see the peptide in center of the x-y plane while interacting with > the polar groups? > trjconv has a number of ways to deal with this. Please read trjconv -h. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Centering the system
Hi. You should use the following command to center your protein: trjconv -f trajectory.xtc -o corrected_trajectory.xtc -pbc mol -center -s trajectory.tpr Don't forget to replace "trajectory" with corresponding filenames 2013/10/16 Shima Arasteh > > > Dear gmx users, > > I have a system consist of a lipid bilayer and a peptide. As the initial > configuration, the peptide is located in center of the x-y plane above > lipid bilayer. After running MD, the peptide shows interactions with the > polar groups. It's ok, but the peptide is near one edge of the x-y plane of > the bilayer. I' d like to know if there is any way to use the properties of > the pbc and see the peptide in center of the x-y plane while interacting > with the polar groups? > > Thanks in advance, > Your suggestions would be appreciated. > > Sincerely, > Shima > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Andrew Gonchar Андрей Гончар -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Centering the system
On 10/16/13 8:29 AM, Shima Arasteh wrote: Dear gmx users, I have a system consist of a lipid bilayer and a peptide. As the initial configuration, the peptide is located in center of the x-y plane above lipid bilayer. After running MD, the peptide shows interactions with the polar groups. It's ok, but the peptide is near one edge of the x-y plane of the bilayer. I' d like to know if there is any way to use the properties of the pbc and see the peptide in center of the x-y plane while interacting with the polar groups? trjconv has a number of ways to deal with this. Please read trjconv -h. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
