Re: [gmx-users] How to avoid the error:"Shake blockcrossing nodeboundaries"
Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option "-pd" of mdrun. In this case the automatic particle distribution over the nodes leads to the error: "Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193)" In the previous version 3.3 I used manual balancing with the "-load" option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? I'd suggest updating to 4.0.4 for the copious bug fixes, one of which might solve your problem. I can't think of a good reason offhand why PD or DD should be necessary for non-PBC simulations in vacuo - try both. If you've still got your problem, let us know. Mark Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations. Only PD options is available. But PD has no flexibility to manually redistribute particles over the nodes. As written in the manual "With PD only whole molecules can be assigned to a processor". Does it mean that there is no way to start PD parallel simulations of whole protein? In other words, does it means that there is no way to run parallel simulation of protein in vacuum? You can do it the way all the other programs do: only use constraints on bonds involving H, and reducing the timestep to 1 fs. I try to run MD with only constrained h-bonds (constraints = hbonds) which allow 2fs timestep. The timestep 1fs would be needed if there will be vibrating (unconstrained) h-bonds. But you suggest to use constraints or it was a misprint? This is subject to discussion, see e.g. gromacs manual. Actually, with all bonds constrained 2 fs is already a large time step, and with only bonds containing H constrained 1 fs is also quite large. A further discussion can be found in the P-Lincs paper IIRC (J. Chem. Theor. Comp. 4 (2008) p. 116). Thank you for the reference. The subject is what I would like to know in more details. Regarding the problem that "Shake block crossing node boundaries", the "-load" option implemented in gromacs-3.3.3 seems to remain the most computationally efficient due to the larger, at least technically, 2fs timestep. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to avoid the error: "Shake blockcrossing nodeboundaries"
Igor Leontyev wrote: Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option "-pd" of mdrun. In this case the automatic particle distribution over the nodes leads to the error: "Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193)" In the previous version 3.3 I used manual balancing with the "-load" option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? I'd suggest updating to 4.0.4 for the copious bug fixes, one of which might solve your problem. I can't think of a good reason offhand why PD or DD should be necessary for non-PBC simulations in vacuo - try both. If you've still got your problem, let us know. Mark Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations. Only PD options is available. But PD has no flexibility to manually redistribute particles over the nodes. As written in the manual "With PD only whole molecules can be assigned to a processor". Does it mean that there is no way to start PD parallel simulations of whole protein? In other words, does it means that there is no way to run parallel simulation of protein in vacuum? You can do it the way all the other programs do: only use constraints on bonds involving H, and reducing the timestep to 1 fs. I try to run MD with only constrained h-bonds (constraints = hbonds) which allow 2fs timestep. The timestep 1fs would be needed if there will be vibrating (unconstrained) h-bonds. But you suggest to use constraints or it was a misprint? This is subject to discussion, see e.g. gromacs manual. Actually, with all bonds constrained 2 fs is already a large time step, and with only bonds containing H constrained 1 fs is also quite large. A further discussion can be found in the P-Lincs paper IIRC (J. Chem. Theor. Comp. 4 (2008) p. 116). ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to avoid the error: "Shake blockcrossing nodeboundaries"
Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option "-pd" of mdrun. In this case the automatic particle distribution over the nodes leads to the error: "Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193)" In the previous version 3.3 I used manual balancing with the "-load" option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? I'd suggest updating to 4.0.4 for the copious bug fixes, one of which might solve your problem. I can't think of a good reason offhand why PD or DD should be necessary for non-PBC simulations in vacuo - try both. If you've still got your problem, let us know. Mark Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations. Only PD options is available. But PD has no flexibility to manually redistribute particles over the nodes. As written in the manual "With PD only whole molecules can be assigned to a processor". Does it mean that there is no way to start PD parallel simulations of whole protein? In other words, does it means that there is no way to run parallel simulation of protein in vacuum? You can do it the way all the other programs do: only use constraints on bonds involving H, and reducing the timestep to 1 fs. I try to run MD with only constrained h-bonds (constraints = hbonds) which allow 2fs timestep. The timestep 1fs would be needed if there will be vibrating (unconstrained) h-bonds. But you suggest to use constraints or it was a misprint? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
