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Max number of atoms in a fragment in .mcf
- ozzie787
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7 years 8 months ago #225
by ozzie787
Hello dev's
I have a question regarding an issue I've noticed since installing the29 July release of Cass 1.2 and also on yesterday's updated 4 August release.
The molecule I am simulating is a 35 atom crown ether which only has one fragment.
I am wondering if there is a limit of 20 atoms in a single fragment in the .mcf. When I run Cassandra I receive the following error and traceback:
The error appears to be on line 130 of io_utilities.f90, where the string is beeing read character by character. For clarity I should state the error reports line 132 but I inserted a couple of PRINT lines to let me see what was tripping things up.
Run Conditions:
Cassandra Version 1.2 20160804
Ubuntu 15.04
ifort (IFORT) 13.0.0 20120731
I have a question regarding an issue I've noticed since installing the29 July release of Cass 1.2 and also on yesterday's updated 4 August release.
The molecule I am simulating is a 35 atom crown ether which only has one fragment.
I am wondering if there is a limit of 20 atoms in a single fragment in the .mcf. When I run Cassandra I receive the following error and traceback:
forrtl: severe (408): fort: (2): Subscript #1 of the array LINE_ARRAY has value 21 which is greater than the upper bound of 20
Image PC Routine Line Source
cassandra_intel_o 0000000000B2290E Unknown Unknown Unknown
cassandra_intel_o 0000000000B213A6 Unknown Unknown Unknown
cassandra_intel_o 0000000000AD4762 Unknown Unknown Unknown
cassandra_intel_o 0000000000A9765C Unknown Unknown Unknown
cassandra_intel_o 0000000000A97B71 Unknown Unknown Unknown
cassandra_intel_o 000000000041AE45 io_utilities_mp_p 132 io_utilities.f90
cassandra_intel_o 00000000005ABC16 input_routines_mp 2484 input_routines.f90
cassandra_intel_o 0000000000559C6A input_routines_mp 1334 input_routines.f90
cassandra_intel_o 0000000000780343 nptmc_control_ 93 nptmc_control.f90
cassandra_intel_o 0000000000404E36 MAIN__ 198 main.f90
cassandra_intel_o 000000000040314C Unknown Unknown Unknown
libc.so.6 00007EFEA9EC0A40 Unknown Unknown Unknown
cassandra_intel_o 0000000000403039 Unknown Unknown UnknownThe error appears to be on line 130 of io_utilities.f90, where the string is beeing read character by character. For clarity I should state the error reports line 132 but I inserted a couple of PRINT lines to let me see what was tripping things up.
Run Conditions:
Cassandra Version 1.2 20160804
Ubuntu 15.04
ifort (IFORT) 13.0.0 20120731
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- ryangmullen
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7 years 8 months ago #226
by ryangmullen
Yes, there is an inadvertent 18 atom limit on the number of atoms that can be in a fragment. When each line of the MCF is read, the line is parsed into white space separated entries. Each line has a hard cap of 20 entries.
Depending on your simulation goals, it might be best to specify the crown ether with 0 fragments. What's the environment in which you are simulating the crown ether? Is it solvated in water? A neat liquid? In the gas phase?
Depending on your simulation goals, it might be best to specify the crown ether with 0 fragments. What's the environment in which you are simulating the crown ether? Is it solvated in water? A neat liquid? In the gas phase?
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- ozzie787
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7 years 8 months ago #227
by ozzie787
Ah okay! No worries.
The ether is a neat liquid in the reported simulation ... in later simulations, the plan is to have it as the solvent for a large cage type molecule.
For curiosity, is this an intended change from Cass 1.1?
The ether is a neat liquid in the reported simulation ... in later simulations, the plan is to have it as the solvent for a large cage type molecule.
For curiosity, is this an intended change from Cass 1.1?
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7 years 8 months ago #228
by ryangmullen
In v1.1 that hard cap was raised from 20 to 10,000 in order to read in zeolites as single fragment molecule, but it caused other issues in the fragment routines. Ultimately, we redesigned the code to read in zeolites as molecules with 0 fragments.
We could raise that limit to something more moderate, O(100), but I doubt it will help you much. When single-fragment molecules are regrown, they are given a random orientation. Randomly orienting a molecule as big as a crown ether at liquid density will almost certainly result in core overlap and the move will be rejected.
If you care to start using the development version of cassandra, we could look at generalizing the crank-shaft move and you could use those moves instead regrowth moves to sample intramolecular DOF.
We could raise that limit to something more moderate, O(100), but I doubt it will help you much. When single-fragment molecules are regrown, they are given a random orientation. Randomly orienting a molecule as big as a crown ether at liquid density will almost certainly result in core overlap and the move will be rejected.
If you care to start using the development version of cassandra, we could look at generalizing the crank-shaft move and you could use those moves instead regrowth moves to sample intramolecular DOF.
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7 years 8 months ago #229
by ozzie787
Your explanation makes total sense and clears a few things up in my mind. It also makes sense as to the lack of regrowth moves seen in earlier simulations using V1.1.
After talking to my PI he is happy that we treat everything except inserted species as rigid. So for now no need to move to a development version.
Thanks for you swift help once again with Cassandra
After talking to my PI he is happy that we treat everything except inserted species as rigid. So for now no need to move to a development version.
Thanks for you swift help once again with Cassandra
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