Re: [gmx-users] Protein distance with respect to box walls
Try to use the VMD to directly measure the distance between the protein and box boundary. On Tuesday, December 9, 2014 8:16 AM, Smith, Micholas D. smit...@ornl.gov wrote: Hi James, The utility g_mindist lets you measure the minimum distance between a selection and its periodic image, if what you are trying to do is just confirm that your simulation box is large enough to prevent periodic image effects, this is one way to check. Kind Regards, Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a...@imtech.res.in a...@imtech.res.in Sent: Monday, December 08, 2014 11:39 PM To: Gmx users Subject: Re: [gmx-users] Protein distance with respect to box walls Dear James, I think if you load your system in VMD you can measure the dimensions of protein with something like set sel [atomselect top protein] measure minmax $sel Regards. Amin. On 2014-12-09 08:55, James Lord wrote: Dear Users, I have a protein in a box and was wondering to know how to figure out the protein distance to the box walls? I can see the box dimensions at the end of .gro file but how to know what is (x,y,z) of protein in the box?? any comments? Cheers James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein distance with respect to box walls
Hi, The location of the box boundary is irrelevant in virtually all cases, unlike the distance to the periodic image. Why do you need to know the distance to the box? Note that regardless of box angles the simulation cell will be represented as a cuboid within mdrun anyway. Erik On 9 Dec 2014, at 16:55, xu zhijun simulatio...@yahoo.com wrote: Try to use the VMD to directly measure the distance between the protein and box boundary. On Tuesday, December 9, 2014 8:16 AM, Smith, Micholas D. smit...@ornl.gov wrote: Hi James, The utility g_mindist lets you measure the minimum distance between a selection and its periodic image, if what you are trying to do is just confirm that your simulation box is large enough to prevent periodic image effects, this is one way to check. Kind Regards, Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a...@imtech.res.in a...@imtech.res.in Sent: Monday, December 08, 2014 11:39 PM To: Gmx users Subject: Re: [gmx-users] Protein distance with respect to box walls Dear James, I think if you load your system in VMD you can measure the dimensions of protein with something like set sel [atomselect top protein] measure minmax $sel Regards. Amin. On 2014-12-09 08:55, James Lord wrote: Dear Users, I have a protein in a box and was wondering to know how to figure out the protein distance to the box walls? I can see the box dimensions at the end of .gro file but how to know what is (x,y,z) of protein in the box?? any comments? Cheers James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Protein distance with respect to box walls
Dear Users, I have a protein in a box and was wondering to know how to figure out the protein distance to the box walls? I can see the box dimensions at the end of .gro file but how to know what is (x,y,z) of protein in the box?? any comments? Cheers James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein distance with respect to box walls
Dear James, I think if you load your system in VMD you can measure the dimensions of protein with something like set sel [atomselect top protein] measure minmax $sel Regards. Amin. On 2014-12-09 08:55, James Lord wrote: Dear Users, I have a protein in a box and was wondering to know how to figure out the protein distance to the box walls? I can see the box dimensions at the end of .gro file but how to know what is (x,y,z) of protein in the box?? any comments? Cheers James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
