GROMACS version:version 2021.3-MODIFIED GROMACS modification: Yes
Hi, I have a small system with 87 residues of a protein. And I want to maintain the tertiary structure of the protein, so I came up with some restraints which I am supplying in the topology file under the [bonds] directive. It is as follows
137 1188 6 3.253 8000 271 1125 6 3.043 8000 82 1004 6 1.386 8000 319 979 6 2.600 8000 82 923 6 1.309 8000 7 764 6 2.059 8000 257 662 6 2.415 8000 319 829 6 1.809 8000 151 371 6 1.859 8000 371 500 6 1.752 8000 462 764 6 1.440 8000 923 1049 6 1.770 8000 1004 1188 6 2.215 8000
Initially, I have a water padding of 1 nm (total number of atoms ~ 60k) and without the above restraints the simulation runs fine, but when I add the restraints, I got the following error. So, I am pretty sure that my type 6 restraints are causing the problem.
Fatal error: There is no domain decomposition for 96 ranks that is compatible with the given box and a minimum cell size of 4.21705 nm Change the number of ranks or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition
I have searched the gromacs mailing list and other websites and found that if you increase the water padding (or make the box larger) you can avoid this error. So I tried going for 60-angstrom padding, but still have the same error and my total number of atoms reach close to 700k.
Is there a workaround for this problem? I do not want to simulate a bigger system because of my limited computational resources
I am attaching my log file for the NVT run.