Re: [gmx-users] Domain decomposition error with -rerun

Check the trajectories before and after conversion and make sure that there are no pbc effect, if so fix it. Or do the analysis with the avaible trajectories(may be in VMD with tcl scripts). -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Domain decomposition error with -rerun

Thanks for the reply Mark. On Sat, Apr 28, 2018 at 4:32 PM, Mark Abraham wrote: > Hi, > > Clearly the conversion tool did not produce a file that conforms to the > requirements GROMACS has for specifying periodic boxes. That may not work > well even if you'd run mdrun

Re: [gmx-users] Domain decomposition error with -rerun

Hi, Clearly the conversion tool did not produce a file that conforms to the requirements GROMACS has for specifying periodic boxes. That may not work well even if you'd run mdrun without domain decomposition because the periodicity may not be understood correctly. Find out what was going on and

Re: [gmx-users] Domain decomposition error with -rerun

Yes.. I used VMD for conversion... On Sat, Apr 28, 2018 at 12:50 PM, RAHUL SURESH wrote: > Hi > > Sounds strange to my little knowledge. How I would justify is, it may be > due to the conversion from NAMD [dcd] to Gromacs profile [trr] though not > sure. > > So you have

[gmx-users] Dihedral parameters from QM and MM relaxed surface scans

Hello Gromacs Users, I am trying to reproduce some published forcefield development work. In this paper, dihedral parameters are derived from QM and MM relaxed surface scan data collected on individual small molecules in vacuum. My replication workflow is as follows. The MM relaxed surface scan

Re: [gmx-users] Domain decomposition error with -rerun

Hi Sounds strange to my little knowledge. How I would justify is, it may be due to the conversion from NAMD [dcd] to Gromacs profile [trr] though not sure. So you have converted the file format using VMD? On Sat, Apr 28, 2018 at 12:26 PM, Sahithya S Iyer wrote: > Hi, > >

Re: [gmx-users] Domain decomposition error with -rerun

Hi, Thanks for the reply. I am only doing a rerun of a trajectory that has already evolved without any dynamic load balancing problems. -rerun only recalculates energies right. I don't understand why the same trajectory is giving decomposition error now. On Sat, Apr 28, 2018 at 12:11 PM, RAHUL

Re: [gmx-users] Domain decomposition error with -rerun

Hi. That indicates a problem with dynamic load balancing. Try to build different sizes of the box. On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer wrote: > Hi, > > I am trying to calculate interaction between specific residues using gmx > mdrun -rerun flag. The trajectory

[gmx-users] Domain decomposition error with -rerun

Hi, I am trying to calculate interaction between specific residues using gmx mdrun -rerun flag. The trajectory was in a dcd format, which I converted to a trr file. I get the following error - Domain decomposition has not been implemented for box vectors that have non-zero components in