# Out of range water atom after minimization

Dear all LAMMPS user,

I am trying to simulate a simple simulation of box containing of water. First, I used packmol to generate initial water position.
According to many discussion in the mail list, it is best to do a minimization to relaxing the system. So, I do a minimization before the fix shake command, then running the simulation with nvt integration fix.

Best regards,
Steven

Here’s my input script

Dear all LAMMPS user,

I am trying to simulate a simple simulation of box containing of water. First, I used packmol to generate initial water position (the tolerance distance is 3.4).
According to many discussion in the mail list, it is best to do a minimization to relaxing the system. So, I do a minimization before the fix shake command, then running the simulation with nvt integration fix.
Then this “cannot compute PPPM” error came out. I am sure that I have a bad dynamics due to bad initial condition (I got pressure “NAN” in the step 0).

Is there any advice to fix this problem?

Also, there’s something that confuse me. I’m using packmol to generate water position with tolerance distance 3.4 A and the σ

in my pair coeff is 3.1536. Shouldn’t that tolerance distance far enough that there are no huge force between water molecules?

Best regards,
Steven

Here’s my minimize stats:

Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
0.735615826288 -2.02189166282e+17 -2.02189166282e+17
Force two-norm initial, final = 12.1081 2.86713e+32
Force max component initial, final = 3.51211 2.27645e+32
Final line search alpha, max atom move = 8.06832e-74 1.83671e-41
Iterations, force evaluations = 46 882

and here’s my input script

Dear all LAMMPS user,

I am trying to simulate a simple simulation of box containing of water.
First, I used packmol to generate initial water position.
According to many discussion in the mail list, it is best to do a
minimization to relaxing the system. So, I do a minimization before the fix
shake command, then running the simulation with nvt integration fix.
Then this "cannot compute PPPM" error came out. Is there any advice about
this problem?

have you visualized the system after the minimization?
my guess is that it is totally messed up. you have zero force
constants for both bonds and angles. while those are not needed for MD
with shake, they are *required* for minimization or else your water
can completely disintegrate.

don't you have an adviser? teaching you how to set up MD simulations
properly is the job of an adviser (or one or more colleagues
designated by your adviser), not this mailing list. this is not a
LAMMPS problem.

axel.