[gmx-users] is lincs used with virtual hydrogens?
Thank you Mark, I really appreciate it. -- original message -- On 20/06/2011 1:23 AM, chris.neale at utoronto.ca wrote: Dear Mark: Now I am confused. Your first post indicated that P-LINCS did the angle constraints. But here you indicate that the v-site algorithm does it. No... my second email observed that LINCS warnings can result when v-sites are being used, and I ascribed that effect to the size of the time step. I didn't say v-sites were doing anything with angle constraints. This is probably because my first post was incomplete about the method that I used. Can you please confirm my current understanding? Therefore (A): pdb2gmx -vsite none constraints = h-angles constraint_algorithm = lincs -- P-LINCS constrains all bonds and angles involving hydrogens But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds constraint_algorithm = lincs -- Hydrogens are built as V-sites and P-LINCS constrains all bonds that do not involve hydrogen. Of course, water is treated by SETTLE in both of the above. Please note that I am not concerned about getting LINCS warnings. I probably should not have mentioned that. I am simply trying to figure out exactly how to write my methods section. Both the above are correct understandings. I think you misread my second email. I'd intended to put my parenthetical observation about LINCS in the first email, but forgot to (however you seem to have understood my context fine). Sorry for whatever. :) Mark -- 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] is lincs used with virtual hydrogens?
On 20/06/2011 1:23 AM, chris.ne...@utoronto.ca wrote: Dear Mark: Now I am confused. Your first post indicated that P-LINCS did the angle constraints. But here you indicate that the v-site algorithm does it. No... my second email observed that LINCS warnings can result when v-sites are being used, and I ascribed that effect to the size of the time step. I didn't say v-sites were doing anything with angle constraints. This is probably because my first post was incomplete about the method that I used. Can you please confirm my current understanding? Therefore (A): pdb2gmx -vsite none constraints = h-angles constraint_algorithm = lincs -- P-LINCS constrains all bonds and angles involving hydrogens But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds constraint_algorithm = lincs -- Hydrogens are built as V-sites and P-LINCS constrains all bonds that do not involve hydrogen. Of course, water is treated by SETTLE in both of the above. Please note that I am not concerned about getting LINCS warnings. I probably should not have mentioned that. I am simply trying to figure out exactly how to write my methods section. Both the above are correct understandings. I think you misread my second email. I'd intended to put my parenthetical observation about LINCS in the first email, but forgot to (however you seem to have understood my context fine). Sorry for whatever. :) Mark -- 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
[gmx-users] is lincs used with virtual hydrogens?
Dear Mark: Now I am confused. Your first post indicated that P-LINCS did the angle constraints. But here you indicate that the v-site algorithm does it. This is probably because my first post was incomplete about the method that I used. Can you please confirm my current understanding? Therefore (A): pdb2gmx -vsite none constraints = h-angles constraint_algorithm = lincs -- P-LINCS constrains all bonds and angles involving hydrogens But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds constraint_algorithm = lincs -- Hydrogens are built as V-sites and P-LINCS constrains all bonds that do not involve hydrogen. Of course, water is treated by SETTLE in both of the above. Please note that I am not concerned about getting LINCS warnings. I probably should not have mentioned that. I am simply trying to figure out exactly how to write my methods section. Thank you, Chris. -- original message -- Mark On Sat, Jun 18, 2011 at 4:40 PM, chris.neale at utoronto.ca mailto:chris.neale at utoronto.ca chris.neale at utoronto.ca mailto:chris.neale at utoronto.ca wrote: Thank you Roland. I did use: constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs From looking at the manual, I figured that angle and bond constraints would all be done by LINCS if I had done (A): pdb2gmx -vsite none constraints = h-angles (a combination that I have never tried) But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds It seems possible to me that LINCS is not used but instead the position of the atom is simply built from a mathematical function. Perhaps this all stems from my lack of thorough understanding of LINCS, but it seems to me that there need be no iteration to simply place an atoms based on virtual_sites3 (which are constructed by pdb2gms -hydrogen) For now, I'll simply add a line to state that I built virtual sites for hydrogen atoms to make it clear, but I'd still like to understand the difference between options A and B, above, if you have some time. Thank you again, Chris. On Sat, Jun 18, 2011 at 4:13 PM, chris.neale at utoronto.ca http://utoronto.ca chris.neale at utoronto.ca http://utoronto.ca wrote: Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but that warning message could possibly have been written with the assumption that I used LINCS and not virtual hydrogens. Probably. To make sure check the constraint-algorithm selected in your mdp. BTW: If you want to use large timecheck you should normally use constraints=all-bonds and lincs-order=6. Finally, is there a method that needs to be named or cited in relation to the fact that the angles are now constrained? Is that also done with P-LINCS? This is also done with P-LINCS. Not sure whether one should sign something regarding the construction/usage of v-sites. Roland Thank you, Chris. -- 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
[gmx-users] is lincs used with virtual hydrogens?
Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but that warning message could possibly have been written with the assumption that I used LINCS and not virtual hydrogens. Finally, is there a method that needs to be named or cited in relation to the fact that the angles are now constrained? Is that also done with P-LINCS? Thank you, Chris. -- 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] is lincs used with virtual hydrogens?
On Sat, Jun 18, 2011 at 4:13 PM, chris.ne...@utoronto.ca chris.ne...@utoronto.ca wrote: Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but that warning message could possibly have been written with the assumption that I used LINCS and not virtual hydrogens. Probably. To make sure check the constraint-algorithm selected in your mdp. BTW: If you want to use large timecheck you should normally use constraints=all-bonds and lincs-order=6. Finally, is there a method that needs to be named or cited in relation to the fact that the angles are now constrained? Is that also done with P-LINCS? This is also done with P-LINCS. Not sure whether one should sign something regarding the construction/usage of v-sites. Roland Thank you, Chris. -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
[gmx-users] is lincs used with virtual hydrogens?
Thank you Roland. I did use: constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs From looking at the manual, I figured that angle and bond constraints would all be done by LINCS if I had done (A): pdb2gmx -vsite none constraints = h-angles (a combination that I have never tried) But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds It seems possible to me that LINCS is not used but instead the position of the atom is simply built from a mathematical function. Perhaps this all stems from my lack of thorough understanding of LINCS, but it seems to me that there need be no iteration to simply place an atoms based on virtual_sites3 (which are constructed by pdb2gms -hydrogen) For now, I'll simply add a line to state that I built virtual sites for hydrogen atoms to make it clear, but I'd still like to understand the difference between options A and B, above, if you have some time. Thank you again, Chris. On Sat, Jun 18, 2011 at 4:13 PM, chris.neale at utoronto.ca chris.neale at utoronto.ca wrote: Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but that warning message could possibly have been written with the assumption that I used LINCS and not virtual hydrogens. Probably. To make sure check the constraint-algorithm selected in your mdp. BTW: If you want to use large timecheck you should normally use constraints=all-bonds and lincs-order=6. Finally, is there a method that needs to be named or cited in relation to the fact that the angles are now constrained? Is that also done with P-LINCS? This is also done with P-LINCS. Not sure whether one should sign something regarding the construction/usage of v-sites. Roland Thank you, Chris. -- 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] is lincs used with virtual hydrogens?
My understanding is that the v-site algorithm is used for the virtual sites and LINCS is used for bonds not involving v-sites (and also angles if you choose contraint=angles). On Sat, Jun 18, 2011 at 4:40 PM, chris.ne...@utoronto.ca chris.ne...@utoronto.ca wrote: Thank you Roland. I did use: constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs From looking at the manual, I figured that angle and bond constraints would all be done by LINCS if I had done (A): pdb2gmx -vsite none constraints = h-angles (a combination that I have never tried) But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds It seems possible to me that LINCS is not used but instead the position of the atom is simply built from a mathematical function. Perhaps this all stems from my lack of thorough understanding of LINCS, but it seems to me that there need be no iteration to simply place an atoms based on virtual_sites3 (which are constructed by pdb2gms -hydrogen) For now, I'll simply add a line to state that I built virtual sites for hydrogen atoms to make it clear, but I'd still like to understand the difference between options A and B, above, if you have some time. Thank you again, Chris. On Sat, Jun 18, 2011 at 4:13 PM, chris.neale at utoronto.ca chris.neale at utoronto.ca wrote: Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but that warning message could possibly have been written with the assumption that I used LINCS and not virtual hydrogens. Probably. To make sure check the constraint-algorithm selected in your mdp. BTW: If you want to use large timecheck you should normally use constraints=all-bonds and lincs-order=6. Finally, is there a method that needs to be named or cited in relation to the fact that the angles are now constrained? Is that also done with P-LINCS? This is also done with P-LINCS. Not sure whether one should sign something regarding the construction/usage of v-sites. Roland Thank you, Chris. -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] is lincs used with virtual hydrogens?
On 19/06/2011 6:13 AM, chris.ne...@utoronto.ca wrote: Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? Sure - all the backbone bonds, for starters. I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but that warning message could possibly have been written with the assumption that I used LINCS and not virtual hydrogens. No, it's real. Finally, is there a method that needs to be named or cited in relation to the fact that the angles are now constrained? Is that also done with P-LINCS? Yep. Mark Thank you, Chris. -- 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] is lincs used with virtual hydrogens?
On 19/06/2011 6:56 AM, Roland Schulz wrote: My understanding is that the v-site algorithm is used for the virtual sites and LINCS is used for bonds not involving v-sites (and also angles if you choose contraint=angles). Yep. Also, with the LINCS warning about over-rotation, I get that regularly with initial equilibration under conditions such as yours. It seems that somehow -XH3 groups do this (so far I've only seen it in terminal NH3 and CH3). You can fix it by using a smaller time step for a period, which gives the energy a better chance to equipartition properly. Mark On Sat, Jun 18, 2011 at 4:40 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: Thank you Roland. I did use: constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs From looking at the manual, I figured that angle and bond constraints would all be done by LINCS if I had done (A): pdb2gmx -vsite none constraints = h-angles (a combination that I have never tried) But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds It seems possible to me that LINCS is not used but instead the position of the atom is simply built from a mathematical function. Perhaps this all stems from my lack of thorough understanding of LINCS, but it seems to me that there need be no iteration to simply place an atoms based on virtual_sites3 (which are constructed by pdb2gms -hydrogen) For now, I'll simply add a line to state that I built virtual sites for hydrogen atoms to make it clear, but I'd still like to understand the difference between options A and B, above, if you have some time. Thank you again, Chris. On Sat, Jun 18, 2011 at 4:13 PM, chris.neale at utoronto.ca http://utoronto.ca chris.neale at utoronto.ca http://utoronto.ca wrote: Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but that warning message could possibly have been written with the assumption that I used LINCS and not virtual hydrogens. Probably. To make sure check the constraint-algorithm selected in your mdp. BTW: If you want to use large timecheck you should normally use constraints=all-bonds and lincs-order=6. Finally, is there a method that needs to be named or cited in relation to the fact that the angles are now constrained? Is that also done with P-LINCS? This is also done with P-LINCS. Not sure whether one should sign something regarding the construction/usage of v-sites. Roland Thank you, Chris. -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov http://cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
