Error when generating fragment libraries
- jshah46545
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5 years 5 months ago #551
by jshah46545
Mostafa,
As the script for generating fragment does not currently support fused rings, it incorrectly identifies that the molecule contains 9 fragments. The molecule has the following fragments (any (fused) ring is considered as a fragment along with its exoring atoms) :
Fragment 1: atoms 1-11
Fragment 2: atoms 1, 11, 12
Fragment 3: 11, 12, 13
Fragment 4: 12, 13, 14
Fragment 5: atoms 14-28
If you manually modify the # Fragment_Info and # Fragment_Connectivity sections in the mcf file and rerun the fragment generation script, it might work.
Please let us know if you continue to have issues.
Best,
Jindal
As the script for generating fragment does not currently support fused rings, it incorrectly identifies that the molecule contains 9 fragments. The molecule has the following fragments (any (fused) ring is considered as a fragment along with its exoring atoms) :
Fragment 1: atoms 1-11
Fragment 2: atoms 1, 11, 12
Fragment 3: 11, 12, 13
Fragment 4: 12, 13, 14
Fragment 5: atoms 14-28
If you manually modify the # Fragment_Info and # Fragment_Connectivity sections in the mcf file and rerun the fragment generation script, it might work.
Please let us know if you continue to have issues.
Best,
Jindal
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- mostafa.razavi
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5 years 5 months ago #552
by mostafa.razavi
Jindal,
Thank you for your helpful response. I manually specified Fragment_Info and Fragment_Connectivity sections in mcf file as below:
The script ran successfully, but Cassandra gave an error:
Then I tried considering 13, 14, 15 as a fragment, with the same logic as we consider 1, 11, 12 a fragment. The script and Cassandra both run successfully:
Is the above specification correct? Specifically, have I identified the branch_point values for the first and last fragments correctly?
Thank you for your helpful response. I manually specified Fragment_Info and Fragment_Connectivity sections in mcf file as below:
!index number_of_atoms_in_fragment branch_point other_atoms
# Fragment_Info
5
1 11 1 2 3 4 5 6 7 8 9 10 11
2 3 11 1 12
3 3 12 11 13
4 3 13 12 14
5 15 15 16 17 18 19 20 21 22 23 24 25 26 27 28 14
# Fragment_Connectivity
4
1 1 2
2 2 3
3 3 4
4 4 5The script ran successfully, but Cassandra gave an error:
Number of atoms in species 1 is 28
Number of atoms deleted with frag 1 is 9
Number of atoms deleted with frag 2 is 4
This error occurred in subroutine Get_Fragment_Connectivity_Info on step 0.
Fatal Error. Stopping program.Then I tried considering 13, 14, 15 as a fragment, with the same logic as we consider 1, 11, 12 a fragment. The script and Cassandra both run successfully:
!index number_of_atoms_in_fragment branch_point other_atoms
# Fragment_Info
6
1 11 1 2 3 4 5 6 7 8 9 10 11
2 3 11 1 12
3 3 12 11 13
4 3 13 12 14
5 3 14 13 15
6 15 15 16 17 18 19 20 21 22 23 24 25 26 27 28 14
# Fragment_Connectivity
5
1 1 2
2 2 3
3 3 4
4 4 5
5 5 6Is the above specification correct? Specifically, have I identified the branch_point values for the first and last fragments correctly?
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- mostafa.razavi
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5 years 5 months ago #553
by mostafa.razavi
Also, I realized that in the mcf file generated by mcfgen.py script, atoms 3, 17, and 18 have "ring ring" in the Atom_Info section. I cannot think of a special trait that these atoms might have, other than being part of two rings. If this is true, should 8, 23, and 26 also have "ring ring" instead of "ring"?
# Atom_Info
28
1 CA Ca 12.01070 0.0 LJ 21.000 3.880 ring
2 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
3 C1A 1A 12.01070 0.0 LJ 30.000 3.700 ring ring
4 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
5 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
6 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
7 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
8 C1A 1A 12.01070 0.0 LJ 30.000 3.700 ring
9 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
10 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
11 CH2 H2 14.02660 0.0 LJ 46.000 3.950
12 CH2 H2 14.02660 0.0 LJ 46.000 3.950
13 CH2 H2 14.02660 0.0 LJ 46.000 3.950
14 CH2 H2 14.02660 0.0 LJ 46.000 3.950
15 CA Ca 12.01070 0.0 LJ 21.000 3.880 ring
16 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
17 C1A 1A 12.01070 0.0 LJ 30.000 3.700 ring ring
18 C1A 1A 12.01070 0.0 LJ 30.000 3.700 ring ring
19 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
20 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
21 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
22 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
23 C1A 1A 12.01070 0.0 LJ 30.000 3.700 ring
24 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
25 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
26 C1A 1A 12.01070 0.0 LJ 30.000 3.700 ring
27 CH Ch 13.01864 0.0 LJ 50.500 3.695 ring
28 CH Ch 13.01864 0.0 LJ 50.500 3.695 ringPlease Log in to join the conversation.
- ryangmullen
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5 years 5 months ago #554
by ryangmullen
Hi Mostafa,
Yes, atoms 13, 14, 15 should be identified as their own fragment and everything looks correct in your # Fragment_Info and # Fragment_Connectivity sections.
I think "ring ring" and "ring" will both be read the same by Cassandra. Are you treating fragments 1 and 6 (the fused ring fragments) as flexible or rigid?
Ryan
Yes, atoms 13, 14, 15 should be identified as their own fragment and everything looks correct in your # Fragment_Info and # Fragment_Connectivity sections.
I think "ring ring" and "ring" will both be read the same by Cassandra. Are you treating fragments 1 and 6 (the fused ring fragments) as flexible or rigid?
Ryan
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- mostafa.razavi
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5 years 5 months ago #555
by mostafa.razavi
Thanks Ryan,
I'm simulating this molecule using TraPPE-UA force field, so yes I'm trying to treat the fused rings as rigid. I set all the bonds, and angles to be fixed, but I have dihedrals as you can see in the mcf file.
I'm simulating this molecule using TraPPE-UA force field, so yes I'm trying to treat the fused rings as rigid. I set all the bonds, and angles to be fixed, but I have dihedrals as you can see in the mcf file.
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- mostafa.razavi
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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:
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
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