Re: [gmx-users] Regarding trjconv
Thank you Justin. I tried to define a reference group having the desired orientation and use -fit. But the box rotates as well. I need to keep the box as it is and just rotate the solute. Using -fit prompts me to choose the group for least squares fit and the output, only. When I use -princ in editconf, it orients the crystal in z direction perfectly. The only problem is that the box rotates as well, and is not well aligned along the same direction. Any suggestions? Best, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: zondag 2 december 2018 17:38 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Regarding trjconv On 12/2/18 11:22 AM, Ali Khodayari wrote: > Dear all, > > > > I am trying to re-center and re-orient an md resulted solute in a box. > Yet, I need the box to hold its position and I only need a group of > atoms to align along z-direction. Trjconv centers the group in the box > but the desired sub-group has a slight inclination which is needed to > be oriented along z axis. Is there any particular trick to do this? > Maybe in combination with editconf? > > trjconv -fit with a suitable index group that defines the orientation you want. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Regarding trjconv
On 12/2/18 11:22 AM, Ali Khodayari wrote: Dear all, I am trying to re-center and re-orient an md resulted solute in a box. Yet, I need the box to hold its position and I only need a group of atoms to align along z-direction. Trjconv centers the group in the box but the desired sub-group has a slight inclination which is needed to be oriented along z axis. Is there any particular trick to do this? Maybe in combination with editconf? trjconv -fit with a suitable index group that defines the orientation you want. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Regarding trjconv
Dear all, I am trying to re-center and re-orient an md resulted solute in a box. Yet, I need the box to hold its position and I only need a group of atoms to align along z-direction. Trjconv centers the group in the box but the desired sub-group has a slight inclination which is needed to be oriented along z axis. Is there any particular trick to do this? Maybe in combination with editconf? Best, Ali -- 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] Regarding trjconv
On 11/17/2016 10:19 AM, Justin Lemkul wrote: On 11/17/16 10:13 AM, Apramita Chand wrote: Dear All, Thanks for your explanation, Erik. I just want to know whether applying trjconv will affect my calculations of other values like radial distribution functions ,hydrogen bond properties. Before applying trjconv,my protein molecule appears to be shifted partly out of the box . Should I be applying trjconv in this situation before calculation of properties? Is it necessary at all? Nearly all GROMACS tools handle PBC automatically. Only position-dependent properties like RMSD, RMSF, covariance, etc. are impacted by not accounting for PBC. Anything related to distances like RDF, H-bonds, etc. requires no correction, but even if you do use trjconv, the results should come out the same. -Justin I have also noticed that if use a PBC-corrected .xtc file for hbond against solvent molecules, it will often generate an error or crash the tool, which does not occur without trjconv. Gregory -- 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] Regarding trjconv
On 11/17/16 10:13 AM, Apramita Chand wrote: Dear All, Thanks for your explanation, Erik. I just want to know whether applying trjconv will affect my calculations of other values like radial distribution functions ,hydrogen bond properties. Before applying trjconv,my protein molecule appears to be shifted partly out of the box . Should I be applying trjconv in this situation before calculation of properties? Is it necessary at all? Nearly all GROMACS tools handle PBC automatically. Only position-dependent properties like RMSD, RMSF, covariance, etc. are impacted by not accounting for PBC. Anything related to distances like RDF, H-bonds, etc. requires no correction, but even if you do use trjconv, the results should come out the same. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Regarding trjconv
Dear All, Thanks for your explanation, Erik. I just want to know whether applying trjconv will affect my calculations of other values like radial distribution functions ,hydrogen bond properties. Before applying trjconv,my protein molecule appears to be shifted partly out of the box . Should I be applying trjconv in this situation before calculation of properties? Is it necessary at all? Regards Apramita -- 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] Regarding trjconv
Dear Aparamita, trjconv can enable or preclude subsequent analysis of trajectories, depending on what you want to do. For example, by fitting chosen groups to a reference structure. By centering your protein, you effectively remove all lateral diffusion, so it’s not surprising that a very low diffusion coefficient is reported for the processed trajectory. Kind regards, Erik > On 17 Nov 2016, at 08:53, Apramita Chandwrote: > > Dear All, > I had one doubt regarding g_trjconv which I used to center my protein after > simulation. I got different diffusion values when I used the .xtc file > before and after applying trjconv. Which one should be used? Is trjconv > just for visualisation or is necessary for analysis too? Does it change the > values or interactions in any way? > For example, the diffusion values that I got were > Before trjconv After Trjconv > Urea - 1.6628 2.089 > Protein -0.09270.000108 > Water 2.513 2.59 > > Please advise. Which values should be taken? > > Regards > Apramita > -- > 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] Regarding trjconv
Dear All, I had one doubt regarding g_trjconv which I used to center my protein after simulation. I got different diffusion values when I used the .xtc file before and after applying trjconv. Which one should be used? Is trjconv just for visualisation or is necessary for analysis too? Does it change the values or interactions in any way? For example, the diffusion values that I got were Before trjconv After Trjconv Urea - 1.6628 2.089 Protein -0.09270.000108 Water 2.513 2.59 Please advise. Which values should be taken? Regards Apramita -- 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.