Re: [gmx-users] Fatal error when using Hbond restraints
Robert Johnson wrote: Hello everyone, I'm performing a simulation that includes a 2D infinite SiO2 substrate. I'm not interested in the high frequency motion of the substrate bonds, so I'm applying position restraints to all the SiO2 atoms. I have other molecules in the system such as water and DNA that require hydrogen bond restraints. However, I'm getting the following error when trying to run the system across several nodes: Fatal error: Shake block crossing node boundaries constraint between atoms (1680,1716) The atoms listed are in the substrate. Since I'm already restraining the substrate atoms, I don't really need to constrain the Hbonds in the SiO2. Is there any way to apply Hbond restraints only to a group of atoms? Alternatively, how does Gromacs decide which bonds contain hydrogen? I could just alter the topology file for the substrate to trick Gromacs into thinking that the hydrogens in the SiO2 are really a different type of atom. Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Bob, try using constraints = all-bonds, or make sure that your charge groups overlap with the constraint groups. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fatal error when using Hbond restraints
Robert Johnson wrote: Hello everyone, I'm performing a simulation that includes a 2D infinite SiO2 substrate. I'm not interested in the high frequency motion of the substrate bonds, so I'm applying position restraints to all the SiO2 atoms. I have other molecules in the system such as water and DNA that require hydrogen bond restraints. However, I'm getting the following error when trying to run the system across several nodes: Fatal error: Shake block crossing node boundaries constraint between atoms (1680,1716) The atoms listed are in the substrate. Since I'm already restraining the substrate atoms, I don't really need to constrain the Hbonds in the SiO2. Is there any way to apply Hbond restraints only to a group of atoms? Alternatively, how does Gromacs decide which bonds contain hydrogen? I could just alter the topology file for the substrate to trick Gromacs into thinking that the hydrogens in the SiO2 are really a different type of atom. Thanks, Bob Johnson I'm at this very moment looking at http://bugzilla.gromacs.org/show_bug.cgi?id=110 which reports the same error. You might try to use pbc=full and contraint_algorithm = lincs to circumvent the problem. The problem you have does not arise from the position restraints though, and, by the way, you probably don't need those restraints at all. I don't know what you mean with hbond restraints though... -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error when using Hbond restraints
Hello everyone, I'm performing a simulation that includes a 2D infinite SiO2 substrate. I'm not interested in the high frequency motion of the substrate bonds, so I'm applying position restraints to all the SiO2 atoms. I have other molecules in the system such as water and DNA that require hydrogen bond restraints. However, I'm getting the following error when trying to run the system across several nodes: Fatal error: Shake block crossing node boundaries constraint between atoms (1680,1716) The atoms listed are in the substrate. Since I'm already restraining the substrate atoms, I don't really need to constrain the Hbonds in the SiO2. Is there any way to apply Hbond restraints only to a group of atoms? Alternatively, how does Gromacs decide which bonds contain hydrogen? I could just alter the topology file for the substrate to trick Gromacs into thinking that the hydrogens in the SiO2 are really a different type of atom. Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
