Problem with charged system

Dear Javad,

Could you let us know the type of compiler you used? Do you get the same error in the debug mode too - compiling with Makefile?

Also, if you can send us the input file for water, we will try to replicate the issue you are having.

Jindal

Dear Jindal,

I have not tried the debug mode,and i used the gfortran compiler on a linux machine.
It works fine for constant volume simulations of uncharged systems, but it crashes for cases in which a computationally expensive task such as calculation of Ewald sum or volume attempt is being performed (so, the problem is connected with parallelization scheme).

By the way, the input files for SPC water was the original files in the example directory of the documentation. The attached files are the inputs i used for running TraPEE CO2 and you might want to run it on your machine.

Javad

!**********************************************************************************
!Molecular connectivity file for CO2.pdb
!**********************************************************************************

# Atom_Info
3
1 C1_s1_s1 C 12.0107 0.7 LJ 7 2.8
2 O2_s1_s1 O 15.9994 -0.35 LJ 79 3.05
3 O3_s1_s1 O 15.9994 -0.35 LJ 79 3.05

# Bond_Info
2
1 1 3 fixed 1.16
2 1 2 fixed 1.16

# Angle_Info
1
1 3 1 2 fixed 180

# Dihedral_Info
0

# Fragment_Info
1
1 3 1 3 2

# Improper_Info
0

# Fragment_Connectivity
0


END

---

!*******************************************************************************
! This is an input file for CO2 .
!*******************************************************************************
# Run_Name
TraPPE_CO2

# Sim_Type
NPT_MC

# Nbr_Species
1

# VDW_Style
LJ cut_tail 12.0

# Charge_Style
NONE

# Intra_Scaling
0.0 0.0 0.0 1.0
0.0 0.0 0.0 1.0

# Mixing_Rule
LB

# Seed_Info
80411904 80411904

# Rcutoff_Low
1.0

# Pair_Energy
TRUE

# Molecule_Files
CO2.mcf 100

# Box_Info
1
CUBIC
30.00 30.00 30.00

# Temperature_Info
336.0

# Pressure_Info
100.0

# Move_Probability_Info

# Prob_Translation
0.55
1.0

# Prob_Rotation
0.2
120.0

# Prob_Regrowth
0.245
1.0

# Prob_Volume
0.005
200.0

# Done_Probability_Info

# Start_Type
make_config
100

# Run_Type
Equilibration 100 10

# Average_Info ( 0 == yes, 1 = No)
1

# Frequency_Info
freq_type none
Nthermofreq 1000
Ncoordfreq 10000
MCsteps 1000000
# Done_Frequency_Info

# Property_Info 1 0
Energy_Total
Nmols
Density
Volume
Pressure

# Fragment_Files
species1/frag1/frag1.dat 1

# Bond_Prob_Cutoff
1.0E-10

END

---

Javad,

The water SPC simulation input file in the Examples directory runs without any error for me. So we need to collect more information to locate the part of the code that's throwing the error. As I suggested, please run it in the debug mode and send us the detailed error message, if any, you see.

Jindal

Jindal,
You were right, i think the problem was with my PC. I managed to run Cassandra on a different machine , it works fine for SPC model.

I was going to use Cassandra for simulation of drug-like molecules, usually contain multiple rings , in an Osmotic Ensemble,
but i noticed that Cassandra does not support double rings at the moment.

Also, the web page claims that Cassandra is able to simulate Osmotic Ensemble(OS) , and the tutorial also mentions fugacity in a table listing cassandra input units, but i do not see any input key for fugacity to simulate OS.

Wondering if by OS , you mean two box-two pressure simulation in NPT variant of Gibbs Ensemble.
Because Cassandra is able to assign different pressure to each box , this way the pressure of one of the boxes can be set on the equivalent fugacity to simulate Osmotic Ensemble.

Javad

Javad,

Good to know that you were able to run Cassandra on a different machine.

If the double ring is rigid then you can still run a simulation in Cassandra by treating the fused ring as one fragment.

Osmotic ensemble is currently not supported in the current version of the code. But as you rightly pointed out that one can perform an NPT Gibbs ensemble simulation. If the fugacity vs pressure dependence is known, it can be used to set the pressure.

Jindal