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Error with .inp file
- gandhiforbes
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8 years 8 months ago #34
by gandhiforbes
Dear Sir,
I am trying the simulation with attatched DEE.inp file.
But i am getting the following error message:
anand@anand-GT702AA-ACJ-s3260in:~/Downloads/FlareGet/Cassandra_V1.0$ python /home/anand/Downloads/FlareGet/Cassandra_V1.0/Scripts/Frag_Library_Setup/library_setup.py DEE.inp DEE.pdb
*********Cassandra setup*********
Cassandra location: /home/anand/Downloads/FlareGet/Cassandra_V1.0/DEE.inp
Scanning input file...
Traceback (most recent call last):
File "/home/anand/Downloads/FlareGet/Cassandra_V1.0/Scripts/Frag_Library_Setup/library_setup.py", line 216, in <module>
nbr_boxes = int(linecache.getline(input_file,box_info_line+1))
NameError: name 'box_info_line' is not defined
anand@anand-GT702AA-ACJ-s3260in:~/Downloads/FlareGet/Cassandra_V1.0$
How to solve this problem?
I am trying the simulation with attatched DEE.inp file.
But i am getting the following error message:
anand@anand-GT702AA-ACJ-s3260in:~/Downloads/FlareGet/Cassandra_V1.0$ python /home/anand/Downloads/FlareGet/Cassandra_V1.0/Scripts/Frag_Library_Setup/library_setup.py DEE.inp DEE.pdb
*********Cassandra setup*********
Cassandra location: /home/anand/Downloads/FlareGet/Cassandra_V1.0/DEE.inp
Scanning input file...
Traceback (most recent call last):
File "/home/anand/Downloads/FlareGet/Cassandra_V1.0/Scripts/Frag_Library_Setup/library_setup.py", line 216, in <module>
nbr_boxes = int(linecache.getline(input_file,box_info_line+1))
NameError: name 'box_info_line' is not defined
anand@anand-GT702AA-ACJ-s3260in:~/Downloads/FlareGet/Cassandra_V1.0$
How to solve this problem?
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- ryangmullen
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- gandhiforbes
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8 years 8 months ago #41
by gandhiforbes
Please find the following:
Input file::::
! This is the input file for GEMC simulation of diethylether at 343.15 K
# Run_Name
DEE
!
# Sim_Type
GEMC
!
# Nbr_Species
1
!
# VDW_Style
LJ cut_tail 14.0
LJ cut_tail 14.0
!
# Rcutoff_Low
1.0
!
# Mixing_Rule
LB
!
# Charge_Style
coul Ewald 14.0 0.000001
coul Ewald 14.0 0.000001
!
# Intra_Scaling
0.0 0.0 0.0 1.0
0.0 0.0 0.0 1.0
!
# Molecule_Files
DEE.mcf 300
!
#Box_Info
2
CUBIC
35.2911 35.2911 35.2911
CUBIC
92.5596 92.5596 92.5596
!
# Temperature_Info
343.15 343.15
!
# Seed_Info
200 24000
!
# Move_Probability_Info
# Prob_Translation
0.30
0.4265
14.0
# Prob_Rotation
0.30
38.0
180.0
# Prob_Regrowth
0.30
1.0
# Prob_Volume
0.005
900.0
900.0
# Prob_Swap
0.095
insertion method
reservoir
# Done_Probability_Info
!
# Pressure_Info
1.0
# Bond_Prob_Cutoff
1.0E-10
# CBMC_Info
kappa_ins 12
kappa_rot 0
kappa_dih 12
rcut_cbmc 6.5 6.5
# Start_Type
read_old
Init_Config/nvt_liq.xyz
Init_Config/nvt_vap.xyz
!
# Run_Type
Production 5000 100
!
# Average_Info ( 0 == yes, 1 = No)
1
# Frequency_Info
freq_type none
Nthermofreq 300
Ncoordfreq 3000
MCsteps 3000
# Done_Frequency_Info
!
# Property_Info 1
Energy_Total
Nmols
Volume
# Property_Info 2
Energy_Total
Nmols
Volume
Pressure
# Fragment_Files
species1/frag1/frag1.dat 1
species1/frag2/frag2.dat 2
species1/frag3/frag3.dat 3
# Pair_Energy
TRUE
END
pdb file
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.2
HETATM 1 C LIG 1 -3.495 0.602 -0.000 1.00 0.00 C CH3
HETATM 2 C LIG 1 -2.125 -0.043 0.000 1.00 0.00 C CH2
HETATM 3 O LIG 1 -1.144 0.947 -0.000 1.00 0.00 O
HETATM 4 C LIG 1 0.062 0.248 -0.000 1.00 0.00 C CH2
HETATM 5 C LIG 1 1.215 1.229 -0.000 1.00 0.00 C CH3
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5
CONECT 5 4
MASTER 0 0 0 0 0 0 0 0 5 0 5 0
END
mcf file
!**********************************************************************************
!Molecular connectivity file for DEE.pdb
!**********************************************************************************
# Atom_Info
5
1 C1_s1_s1 C 15 0.000 LJ 98.0 3.750
2 C2_s1_s1 C 14 0.250 LJ 46.0 3.950
3 O3_s1_s1 O 16 -0.500 LJ 55.0 2.800
4 C4_s1_s1 C 14 0.250 LJ 46.0 3.950
5 C5_s1_s1 C 15 0.000 LJ 98.0 3.750
# Bond_Info
4
1 1 2 fixed 1.540
2 2 3 fixed 1.410
3 3 4 fixed 1.410
4 4 5 fixed 1.540
# Angle_Info
3
1 1 2 3 harmonic 112.0
2 2 3 4 harmonic 112.0
3 3 4 5 harmonic 112.0
# Dihedral_Info
2
1 1 2 3 4 OPLS 0.00000 6.03056 -1.35809 4.64087
2 2 3 4 5 OPLS 0.00000 6.03056 -1.35809 4.64087
# Fragment_Info
1
1 5 1 2 3 4 5
# Improper_Info
0
# Fragment_Connectivity
0
END
Thanks and regards,
Anand Bharti
Input file::::
! This is the input file for GEMC simulation of diethylether at 343.15 K
# Run_Name
DEE
!
# Sim_Type
GEMC
!
# Nbr_Species
1
!
# VDW_Style
LJ cut_tail 14.0
LJ cut_tail 14.0
!
# Rcutoff_Low
1.0
!
# Mixing_Rule
LB
!
# Charge_Style
coul Ewald 14.0 0.000001
coul Ewald 14.0 0.000001
!
# Intra_Scaling
0.0 0.0 0.0 1.0
0.0 0.0 0.0 1.0
!
# Molecule_Files
DEE.mcf 300
!
#Box_Info
2
CUBIC
35.2911 35.2911 35.2911
CUBIC
92.5596 92.5596 92.5596
!
# Temperature_Info
343.15 343.15
!
# Seed_Info
200 24000
!
# Move_Probability_Info
# Prob_Translation
0.30
0.4265
14.0
# Prob_Rotation
0.30
38.0
180.0
# Prob_Regrowth
0.30
1.0
# Prob_Volume
0.005
900.0
900.0
# Prob_Swap
0.095
insertion method
reservoir
# Done_Probability_Info
!
# Pressure_Info
1.0
# Bond_Prob_Cutoff
1.0E-10
# CBMC_Info
kappa_ins 12
kappa_rot 0
kappa_dih 12
rcut_cbmc 6.5 6.5
# Start_Type
read_old
Init_Config/nvt_liq.xyz
Init_Config/nvt_vap.xyz
!
# Run_Type
Production 5000 100
!
# Average_Info ( 0 == yes, 1 = No)
1
# Frequency_Info
freq_type none
Nthermofreq 300
Ncoordfreq 3000
MCsteps 3000
# Done_Frequency_Info
!
# Property_Info 1
Energy_Total
Nmols
Volume
# Property_Info 2
Energy_Total
Nmols
Volume
Pressure
# Fragment_Files
species1/frag1/frag1.dat 1
species1/frag2/frag2.dat 2
species1/frag3/frag3.dat 3
# Pair_Energy
TRUE
END
pdb file
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.2
HETATM 1 C LIG 1 -3.495 0.602 -0.000 1.00 0.00 C CH3
HETATM 2 C LIG 1 -2.125 -0.043 0.000 1.00 0.00 C CH2
HETATM 3 O LIG 1 -1.144 0.947 -0.000 1.00 0.00 O
HETATM 4 C LIG 1 0.062 0.248 -0.000 1.00 0.00 C CH2
HETATM 5 C LIG 1 1.215 1.229 -0.000 1.00 0.00 C CH3
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5
CONECT 5 4
MASTER 0 0 0 0 0 0 0 0 5 0 5 0
END
mcf file
!**********************************************************************************
!Molecular connectivity file for DEE.pdb
!**********************************************************************************
# Atom_Info
5
1 C1_s1_s1 C 15 0.000 LJ 98.0 3.750
2 C2_s1_s1 C 14 0.250 LJ 46.0 3.950
3 O3_s1_s1 O 16 -0.500 LJ 55.0 2.800
4 C4_s1_s1 C 14 0.250 LJ 46.0 3.950
5 C5_s1_s1 C 15 0.000 LJ 98.0 3.750
# Bond_Info
4
1 1 2 fixed 1.540
2 2 3 fixed 1.410
3 3 4 fixed 1.410
4 4 5 fixed 1.540
# Angle_Info
3
1 1 2 3 harmonic 112.0
2 2 3 4 harmonic 112.0
3 3 4 5 harmonic 112.0
# Dihedral_Info
2
1 1 2 3 4 OPLS 0.00000 6.03056 -1.35809 4.64087
2 2 3 4 5 OPLS 0.00000 6.03056 -1.35809 4.64087
# Fragment_Info
1
1 5 1 2 3 4 5
# Improper_Info
0
# Fragment_Connectivity
0
END
Thanks and regards,
Anand Bharti
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- ryangmullen
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8 years 8 months ago - 8 years 8 months ago #42
by ryangmullen
Hi Anand,
You are getting that error because your input file has the keyword "#Box_Info" without the required space after the #. If you instead use "# Box_Info" it should resolve the issue.
By the way, in your mcf file you define diethylether as a single (rigid) fragment with the lines:
________________________________________________________
# Fragment_Info
1
1 5 1 2 3 4 5
# Fragment_Connectivity
0
________________________________________________________
To instead simulate flexible diethylether you will instead need to define it as 3 fragments. The following lines should work for your case:
________________________________________________________
# Fragment_Info
3
1 3 2 1 3
2 3 3 2 4
3 3 4 3 5
# Fragment_Connectivity
2
1 1 2
2 2 3
________________________________________________________
Hope that helps!
You are getting that error because your input file has the keyword "#Box_Info" without the required space after the #. If you instead use "# Box_Info" it should resolve the issue.
By the way, in your mcf file you define diethylether as a single (rigid) fragment with the lines:
________________________________________________________
# Fragment_Info
1
1 5 1 2 3 4 5
# Fragment_Connectivity
0
________________________________________________________
To instead simulate flexible diethylether you will instead need to define it as 3 fragments. The following lines should work for your case:
________________________________________________________
# Fragment_Info
3
1 3 2 1 3
2 3 3 2 4
3 3 4 3 5
# Fragment_Connectivity
2
1 1 2
2 2 3
________________________________________________________
Hope that helps!
Last Edit: 8 years 8 months ago by ryangmullen.
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- gandhiforbes
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8 years 8 months ago #44
by gandhiforbes
Thanks. With your suggestion, i was able to sort out the problem.
But now i am getting the following error at the last step of starting the simulation.
anand@anand-GT702AA-ACJ-s3260in:~/Downloads/FlareGet/Cassandra_V1.0$ /home/anand/Downloads/FlareGet/Cassandra_V1.0/Src/cassandra_gfortran.exe DEE.inp
Beginning Cassandra Simulation
At line 469 of file read_write_checkpoint.f90 (unit = 120, file = 'PDW�PDW�')
Fortran runtime error: File 'Init_Config/nvt_liq.xyz' does not exist
anand@anand-GT702AA-ACJ-s3260in:~/Downloads/FlareGet/Cassandra_V1.0$
The programme is asking for file 'Init_Config/nvt_liq.xyz'. how to get this file?
thanks.
But now i am getting the following error at the last step of starting the simulation.
anand@anand-GT702AA-ACJ-s3260in:~/Downloads/FlareGet/Cassandra_V1.0$ /home/anand/Downloads/FlareGet/Cassandra_V1.0/Src/cassandra_gfortran.exe DEE.inp
Beginning Cassandra Simulation
At line 469 of file read_write_checkpoint.f90 (unit = 120, file = 'PDW�PDW�')
Fortran runtime error: File 'Init_Config/nvt_liq.xyz' does not exist
anand@anand-GT702AA-ACJ-s3260in:~/Downloads/FlareGet/Cassandra_V1.0$
The programme is asking for file 'Init_Config/nvt_liq.xyz'. how to get this file?
thanks.
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8 years 8 months ago #45
by ryangmullen
It is looking for that file because your input file tells it to, with these lines:
__________________________________________________________
# Start_Type
read_old
Init_Config/nvt_liq.xyz
Init_Config/nvt_vap.xyz
__________________________________________________________
you could generate these files by first running separate NVT simulations for each phase, or you can create a new configuration with, say, 100 molecules in the liquid phase and 20 in the gas phase with these lines:
__________________________________________________________
# Start_Type
make_config
100 20
__________________________________________________________
__________________________________________________________
# Start_Type
read_old
Init_Config/nvt_liq.xyz
Init_Config/nvt_vap.xyz
__________________________________________________________
you could generate these files by first running separate NVT simulations for each phase, or you can create a new configuration with, say, 100 molecules in the liquid phase and 20 in the gas phase with these lines:
__________________________________________________________
# Start_Type
make_config
100 20
__________________________________________________________
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