Dear LAMMPS users,
I am using moltemplate to create the data file for LAMMPS by following the example "Building a simple polymer (using the OPLSAA force field)".
The attached system.data is the initial configuration for simulations, it can be read by VMD correctly by the command:
topo readlammpsdata system.data full
VMD does show what I desire.
Then I want LAMMPS to write a new data file after each 1E6 steps by the command:
label loopi
variable i loop 10
run 1000000
write_data system_after_nvt_$i.data
next i
jump SELF loopi
clear
While the box is periodic, and the size of the simulation box is supposed to be:
-100.0 100.0 xlo xhi
-100.0 100.0 ylo yhi
0.0 4.0 zlo zhi
I checked the position information of molecules in system_after_nvt_2.data**,** all molecules are in the simulation box.
But when I use VMD to read the new data file, VMD gives the size:
{-115.0782699584961 -112.42899322509766 -65.6171875} {116.6857681274414 111.63589477539063 80.05809783935547}
VMD does not show the configuration correctly neither.
Best wishes,
Wei
system.data (2.38 MB)
system_after_nvt_2.data (4.01 MB)
Dear LAMMPS users,
I am using moltemplate to create the data file for LAMMPS by following the
example "Building a simple polymer (using the OPLSAA force field)".
The attached system.data is the initial configuration for simulations, it
can be read by VMD correctly by the command:
topo readlammpsdata system.data full
VMD does show what I desire.
Then I want LAMMPS to write a new data file after each 1E6 steps by the
command:
label loopi
variable i loop 10
run 1000000
write_data system_after_nvt_$i.data
next i
jump SELF loopi
clear
While the box is periodic, and the size of the simulation box is supposed to
be:
-100.0 100.0 xlo xhi
-100.0 100.0 ylo yhi
0.0 4.0 zlo zhi
I checked the position information of molecules in system_after_nvt_2.data,
all molecules are in the simulation box.
But when I use VMD to read the new data file, VMD gives the size:
{-115.0782699584961 -112.42899322509766 -65.6171875} {116.6857681274414
111.63589477539063 80.05809783935547}
VMD does not show the configuration correctly neither.
it works for me. do you use current versions of VMD and the topotools plugin?
axel.