Hi,
Quick nitpick... Justin's right on the important points, but note that
mdrun -nt may (or may not) use domain decomposition depending on the .tpr
settings and the way GROMACS was configured. (e.g. a build with OpenMP and
thread-MPI is permitted to use either, and the latter triggers the use of
Dear Justin
Thanks for the reply.
If that's the case what position of atoms the coordinates in trr file
represents?. If I got you right, the coordinates in trr file neither get
along with the mdrun generated gro file due to domain decomposition (hence
broken molecules) nor with the trjconv
On 8/24/15 5:39 AM, anu chandra wrote:
Dear Justin
Thanks for the reply.
If that's the case what position of atoms the coordinates in trr file
represents?. If I got you right, the coordinates in trr file neither get
along with the mdrun generated gro file due to domain decomposition (hence
On 8/19/15 7:22 AM, anu chandra wrote:
Dear Gromacs users,
I just noticed that during simulation 'mdrun' writes gro file in two
formats - one with broken molecules at the boundaries and other one where
surface molecules are perfectly wrapped. Interestingly, this difference in
format depends
Dear Gromacs users,
I just noticed that during simulation 'mdrun' writes gro file in two
formats - one with broken molecules at the boundaries and other one where
surface molecules are perfectly wrapped. Interestingly, this difference in
format depends on where I run the simulation - either in a
