Different parameters for the same group
- pobhomri
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5 years 5 months ago #557
by pobhomri
Dear Cassandra developers and users.
I'm attempting to work with a triacylglycerol molecule for simulating its liquid-liquid equilibrium with organic solvents.
I'm using two different force fields: one for the polar section and another for the non-polar part of the molecule. However, each section has CH2 groups, and each force field has different values for its parameters. Also, in the polar part, there are parameters for a CH2 bonded to an O and different parameters for a CH2 bonded to a C=O.
Thus, I'm wondering if I can rename the CH2 group (for example, CH2pO for the polar part bonded to an O) and implement the various parameters for the different nonbonded CH2 types.
Thank you so much in advance.
Perci Homrich.
Postdoctoral researcher at the University of São Paulo - Brazil.
I'm attempting to work with a triacylglycerol molecule for simulating its liquid-liquid equilibrium with organic solvents.
I'm using two different force fields: one for the polar section and another for the non-polar part of the molecule. However, each section has CH2 groups, and each force field has different values for its parameters. Also, in the polar part, there are parameters for a CH2 bonded to an O and different parameters for a CH2 bonded to a C=O.
Thus, I'm wondering if I can rename the CH2 group (for example, CH2pO for the polar part bonded to an O) and implement the various parameters for the different nonbonded CH2 types.
Thank you so much in advance.
Perci Homrich.
Postdoctoral researcher at the University of São Paulo - Brazil.
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- ryangmullen
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5 years 5 months ago #559
by ryangmullen
Hi Perci,
You can name atom types anything you want, though Cassandra v1.2 does have a six-character limit. For example, you might try to input three atom types CH2pO, CH2npO1, CH2npO2. However, since the last two atom types start with the same six-character string ("CH2npO"), then Cassandra will read them as the same atom type. (CH2pO will still be read as a separate atom type, though). This six-character restriction will be relaxed in v1.3+. Additionally, if you include the section
# Verbose_Log
true
then Cassandra will output the names and parameters of each atom type. You can use it to confirm that Cassandra is reading your CH2 atom types differently.
Ryan
You can name atom types anything you want, though Cassandra v1.2 does have a six-character limit. For example, you might try to input three atom types CH2pO, CH2npO1, CH2npO2. However, since the last two atom types start with the same six-character string ("CH2npO"), then Cassandra will read them as the same atom type. (CH2pO will still be read as a separate atom type, though). This six-character restriction will be relaxed in v1.3+. Additionally, if you include the section
# Verbose_Log
true
then Cassandra will output the names and parameters of each atom type. You can use it to confirm that Cassandra is reading your CH2 atom types differently.
Ryan
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