Problem in calculating VdW Energy

That was my fault definitely and i see it now.

Yet with using the latest msi2lmp tool, the problem is same with the VdW energy values. LAMMPS still calculates it as -88.71 .

The .car, mdf and latest data files are attached. (359 KB)

stablyapi.mdf (404 KB) (1.44 MB)

I tried to run the simulations with a 50 A cut off now. Both softwares calculated same value for the VdW energy.

Yet i need to resolve the problem for 15 A cut off as i will have further work on this structure.

Hi Marcel

I am afraid I don’t quite remember your earlier email, but I think that you are using Forcite. I am not familiar with how it handles cutoffs, but Accelrys often used to use group-based cutoffs rather than atom-based as LAMMPS does. Such a subtlety would make small differences at the shorter cutoff distances. The other thought are the long-range corrections – are you using them in both codes and are they added in the vdW term in one code but separate in the other?



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Here is my first mail, it may answer most of your questions. I use Forcite Module with Atom based VdW calculations with a 15 A cut off.

Thanks for your response.



I use Materials Studio and LAMMPS simultaneously for a polyimide.

The problem i have is that, while MS Forcite module calculates my structure’s VdW energy as -78.516, in LAMMPS i have -88.7126.

I have checked my pair parameters for so many times and there are no problems in them.

I use pcff as force-field and my input file looks like;


units real
boundary p p p
atom_style full

pair_style lj/class2/coul/long 15
kspace_style ewald 1.0e-004
special_bonds lj 0.0 0.0 1.0 coul 0.0 0.0 1.0

bond_style class2
angle_style class2
dihedral_style class2
improper_style class2

neighbor 2.0 bin
neigh_modify every 1 delay 2 check yes page 100000000 one 100000

read_data stablyapi.lammps05
#read_restart TR-m-p.restart.3000000

velocity all create 308.0 4928459 rot yes dist gaussian

thermo_style multi
thermo 10000


dump 1 all custom 100000 6fdadam760.lammpstrj id type xs ys zs ix iy iz

restart 100000 stblypn.restart

timestep 1
fix 1 all npt temp 308 308 20 iso 1 1 1000.0
run 10000

I look at the VdW value at step 0.

I suspect that this may be due to the long range VdW truncations, yet could not find a solution for it.