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Problems with running GEMC_npt:Overlap detected in the starting structure
- Tang Ziqian
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7 years 4 months ago #270
by Tang Ziqian
I was trying to use the gemc_npt to simulate the absorption of CO2 in ILs.I,however,ran into tough problems when the simulation began.The following is my problem:
********************************************************************************
************************ Begin Cassandra simulation ****************************
********************************************************************************
Initial configuration
********************************************************************************
Inserting 250 molecules of species 1
Inserting 250 molecules of species 2
Inserting 500 molecules of species 3
Inserting 150 molecules of species 4
********************************************************************************
Compute total energy
********************************************************************************
************ERROR************
Overlap detected in the starting structure
Start type make_config
This error occurred in subroutine Main on step 0.
Fatal Error. Stopping program.
I am now wondering if there is something wrong with my initial pdb file or something else.I would be much grateful for your kind help.And any discussion is welcome.
********************************************************************************
************************ Begin Cassandra simulation ****************************
********************************************************************************
Initial configuration
********************************************************************************
Inserting 250 molecules of species 1
Inserting 250 molecules of species 2
Inserting 500 molecules of species 3
Inserting 150 molecules of species 4
********************************************************************************
Compute total energy
********************************************************************************
************ERROR************
Overlap detected in the starting structure
Start type make_config
This error occurred in subroutine Main on step 0.
Fatal Error. Stopping program.
I am now wondering if there is something wrong with my initial pdb file or something else.I would be much grateful for your kind help.And any discussion is welcome.
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- emarin
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7 years 4 months ago #271
by emarin
Hello Tang,
Could you try decreasing the R_cutlow option to maybe 1 Angstrom? The R_cutlow option is used to prevent overlaps from occurring. However, problems might occur when distances between non bonded intra molecular interaction sites are less than the specified R_cutlow.
If this does not work, could you provide more details on your system?
Thanks!
Could you try decreasing the R_cutlow option to maybe 1 Angstrom? The R_cutlow option is used to prevent overlaps from occurring. However, problems might occur when distances between non bonded intra molecular interaction sites are less than the specified R_cutlow.
If this does not work, could you provide more details on your system?
Thanks!
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- ryangmullen
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7 years 4 months ago - 7 years 4 months ago #272
by ryangmullen
Hi Tang,
This problem can occur in make_config when the specified starting density is too high. Cassandra will reject attempts to place atoms closer than Rcutoff_low, but the placement of later molecules can raise the energy of early-placed molecules above maximum energy threshold ( = 708 kT). For example, molecule 1 is placed in an empty box and is later surrounded by molecules 5, 22, 38, and 52. As each of these molecules is placed, the interaction energy of molecule 1 increases. If the interaction energy of molecule 1 with other molecules increases above 708 kT, then when you attempt to move molecule 1 (or maybe even when the total initial energy is computed) Cassandra will throw the error you are seeing.
If this is the source of your error, I recommend increasing Rcutoff_low to keep the molecules a little further apart. However, if Rcutoff_low is too high, make_config will not be able to place all the molecules you ask for. In which case you will need to start with lower density (either fewer initial molecules or a initial larger box).
Ryan
This problem can occur in make_config when the specified starting density is too high. Cassandra will reject attempts to place atoms closer than Rcutoff_low, but the placement of later molecules can raise the energy of early-placed molecules above maximum energy threshold ( = 708 kT). For example, molecule 1 is placed in an empty box and is later surrounded by molecules 5, 22, 38, and 52. As each of these molecules is placed, the interaction energy of molecule 1 increases. If the interaction energy of molecule 1 with other molecules increases above 708 kT, then when you attempt to move molecule 1 (or maybe even when the total initial energy is computed) Cassandra will throw the error you are seeing.
If this is the source of your error, I recommend increasing Rcutoff_low to keep the molecules a little further apart. However, if Rcutoff_low is too high, make_config will not be able to place all the molecules you ask for. In which case you will need to start with lower density (either fewer initial molecules or a initial larger box).
Ryan
Last Edit: 7 years 4 months ago by ryangmullen.
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