Thank you professor Justin.
Firstly, I get a true trajectory (stress.trr) from Gromacs 5.0.5 besides the
water.gro, water.top, and nvt.mdp files. Then read the these files with a
custom Gromacs 4.5.5 to calculate local pressure:
grompp_LS -f
nvt.mdp -c water.gro
-p water.top -o
topol.tpr
Dear all,
I used Gromacs 5.0.5 to generate a trajectory of polarizable water system with
SWM4-NDP model, and then tried to use a custom version Gromacs 4.5.5 to
calculate local pressure of the system. When I generate the .tpr file with
Gromacs 4.5.5, an error coccurs:
Fatal error:
Incorrect
On 8/20/15 1:03 PM, 折晓会 wrote:
Dear all,
I used Gromacs 5.0.5 to generate a trajectory of polarizable water system with
SWM4-NDP model, and then tried to use a custom version Gromacs 4.5.5 to
calculate local pressure of the system. When I generate the .tpr file with
Gromacs 4.5.5, an error
On 8/20/15 6:05 PM, 折晓会 wrote:
Thank you professor Justin! I solved this error which comes from the decimals
of the box dimensions. Initially, my box dimensions are 4.5*4.5*16 nm3 and the
local pressure calculation does not work, but after I change them to be
integers 4*4*16 nm3 in the gro
On 8/20/15 4:01 PM, 折晓会 wrote:
Thank you professor Justin! I solved this error with your suggestion.
When I use mdrun -rerun to calculate the local pressure, another error occurs:
Fatal error:
Rerun trajectory frame step 60 time 600.00 has too small box dimensions
What does this
Thank you professor Justin! I solved this error with your suggestion.
When I use mdrun -rerun to calculate the local pressure, another error occurs:
Fatal error:
Rerun trajectory frame step 60 time 600.00 has too small box dimensions
What does this mean?
Best wishes,
Xiaohui
Date:
Thank you professor Justin! I solved this error which comes from the decimals
of the box dimensions. Initially, my box dimensions are 4.5*4.5*16 nm3 and the
local pressure calculation does not work, but after I change them to be
integers 4*4*16 nm3 in the gro file, the simulation works. It is
