Error when generating fragment libraries

mostafa.razavi
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Junior Member

5 years 5 months ago #558 by mostafa.razavi

Dear Ryan and Jindal,

I'm trying to reproduce GEMC results of a recent paper by Yiannourakou titled "United atom forcefield for vapor-liquid equilibrium (VLE) properties of cyclic and polycyclic compounds from Monte Carlo simulations" for the above molecule (1-naphthalenyl,4-phenanthrenyl butane). At 950 K, this paper reports rhoL=640 kg/m^3 and rhoV=19.3 kg/m^3. Looking at the output prp file, after 30 million MC steps, both boxes reach to similar liquid-like density (rho=220 kg/m^3) with roughly the same number of molecules in each box. I was wondering if you guys can comment on why this is happening. I used several other combination of numbers in the Prob_Volume section but they all resulted in the same results. Here is what my input file looks like:

# Run_Name
gemc.out
!------------------------------------------------------------------------------

# Sim_Type
gemc
!------------------------------------------------------------------------------

# Nbr_Species
1
!------------------------------------------------------------------------------

# VDW_Style
lj   cut_tail   14.00
lj   cut_tail   28.00
!------------------------------------------------------------------------------

# Rcutoff_Low
2.0
!------------------------------------------------------------------------------

# Molecule_Files
1-p-4-n-B.mcf 300
!----------------------------------------------------------one line per species

# Box_Info
2
cubic
61.0

cubic
196.0
!-------------------------------------------------------line 1: number of boxes
!--------------------------------------------------------------line 2: box type
!--------------------------------------------------------------line 3: box size
!--------------------------------------------------------------repeat for second box

# Temperature_Info
950.0
950.0
!----------------------------------------------------------one temperature per box

# Move_Probability_Info

# Prob_Translation 
0.30
0.50
14.0

# Prob_Rotation
0.30
30.0
180.0

# Prob_Regrowth
0.30
1.0

# Prob_Volume
0.02
9000.0
300000.0

# Prob_Swap
0.08
cbmc

# Done_Probability_Info
!---------------------one line for each box and one entry/line for each species
!-----------------------------------------each molecule moves per volume change

# Start_Type
make_config 250
make_config 50
!--------make_config: one line for each species and one entry/line for each box
!------------------------------------------------------------read_old: filename
!----------------------------------------------------------checkpoint: filename

# Run_Type
equilibration 3333 100
!-------------------------Equilibration: update maximum widths every 100 steps/update maximum
!-------------------------volume displacement every 100 steps


# Simulation_Length_Info
units        steps
prop_freq    1000
coord_freq   1000000
run          30000000
!------------------ simulation length every 2200 steps, XYZ output every 2200 steps, property
!---------------------------------------output every 100 steps

# Seed
356225 1254874
!------------------------------------------------------------------------------

# Property_Info 1
energy_total
pressure
density
volume
energy_lj
energy_elec
energy_intra
enthalpy
nmols
mass_density
!------------------------------------------------------------------------------

# Property_Info 2
energy_total
pressure
density
volume
energy_lj
energy_elec
energy_intra
enthalpy
nmols
mass_density
!------------------------------------------------------------------------------

# CBMC_Info
kappa_ins 12
kappa_rot 0
kappa_dih 10
rcut_cbmc 6.5 6.5
!------------------------------------------------------------------------------

# Pair_Energy
TRUE
!------------------------------------------------------------------------------

# Fragment_Files
species1/frag1/frag1.dat  1
species1/frag2/frag2.dat  2
species1/frag3/frag3.dat  3
species1/frag4/frag4.dat  4
species1/frag5/frag5.dat  5
species1/frag6/frag6.dat  6
!---------------------------------------------------------one line per fragment

END

File Attachment:

File Name: gemc-1p4nB.zip
File Size:7,273 KB

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jshah46545
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Junior Member

5 years 5 months ago #560 by jshah46545

Dear Mostafa,

Is the overall density initially between the vapor and liquid equilibrium densities? This is to ensure that the starting point is in the two-phase region? Do the two boxes have similar number of molecules and hence the volume?

If you were to start with the liquid box with densities slightly lower than the equilibrium liquid density and the vapor box with a density higher than the expected density, what are the results?

Jindal

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ryangmullen
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Administrator

5 years 5 months ago #561 by ryangmullen

Hi Mostafa,

Here's a few things you can try:

run some NPT sims at rhoL and rhoV to verify that that liquid and vapor densities you expect are stable. This will verify that the force field parameters have all been input correctly.
use the equilibrated configurations from the NPT sims to seed your GEMC simulations. I find that make_config gives high energy configurations that need to be thermally relaxed before they can be used in open ensembles.

Hope that helps,
Ryan

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