[lammps-users] (no subject)

Dear users,

I am trying to match the results of Materials Studio with the results of
LAMMPS. On each system, I am running an NPT of 128 molecules of ethanol
for 100 ps using a 1 fs timestep and a PCFF force field at 298 K and 1
atm. Using Materials Studio, my colleague has gotten a final average
density of 0.757 gm/cm3, whereas I am getting a final average density of
0.902 g/cm3 using LAMMPS.

I assumed the density of the ethanol solution could be calculated and
printed using the simple LAMMPS input script lines:

variable mass_g equal mass(all)/6.02e23
variable vol_cm3 equal vol*1.0e-24
variable mydensity equal v_mass/v_vol_cm3

with the thermo lines:

thermo_style custom step v_mydensity
thermo 1000

I there any problem with calculating the density of the ethanol solution
in this manner?

Thank you very much,

Paul

Paul Harten, PhD
P2Tools Design & Development Team Leader
Sustainable Technology Division, Clean Processes Branch
National Risk Management Research Laboratory
Office of Research and Development
U.S. Environmental Protection Agency
26 West Martin Luther King Drive
Cincinnati, Ohio 45268

Paul - I might have asked you this before - did you
do the test where you take a single snapshot (e.g.
the initial state) and run it for 0 timesteps with
both codes and verify that the energy, forces, pressure
are identical? This is a good test of whether you
are running the same ff parameterization in both cases.

Steve

Steve,

Your associate, Aidan Thompson, gave me a similar suggestion to look at
the potential energy, kinetic energy, and pressure as a function of
time.

I will go ahead and do the initial state test you suggested to verify
that the energy, forces and pressure are identical between Materials
Studio and LAMMPS.

Thank you,

Paul

Paul Harten, PhD
P2Tools Design & Development Team Leader
Sustainable Technology Division, Clean Processes Branch
National Risk Management Research Laboratory
Office of Research and Development
U.S. Environmental Protection Agency
26 West Martin Luther King Drive
Cincinnati, Ohio 45268

             "Steve Plimpton"
             <[email protected]
             > To
                                      Paul Harten/CI/USEPA/[email protected]
             12/08/2008 04:25 cc
             PM [email protected]
                                      t
                                                                Subject
                                      Re: [lammps-users] (no subject)
                                                                        
Paul - I might have asked you this before - did you
do the test where you take a single snapshot (e.g.
the initial state) and run it for 0 timesteps with
both codes and verify that the energy, forces, pressure
are identical? This is a good test of whether you
are running the same ff parameterization in both cases.

Steve

Dear users,

I am trying to match the results of Materials Studio with the results

of

LAMMPS. On each system, I am running an NPT of 128 molecules of

ethanol

for 100 ps using a 1 fs timestep and a PCFF force field at 298 K and 1
atm. Using Materials Studio, my colleague has gotten a final average
density of 0.757 gm/cm3, whereas I am getting a final average density

of

0.902 g/cm3 using LAMMPS.

I assumed the density of the ethanol solution could be calculated and
printed using the simple LAMMPS input script lines:

variable mass_g equal mass(all)/6.02e23
variable vol_cm3 equal vol*1.0e-24
variable mydensity equal v_mass_g/v_vol_cm3

with the thermo lines:

thermo_style custom step v_mydensity
thermo 1000

I there any problem with calculating the density of the ethanol

solution