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I was about to substitute your sigma and epsilon values for the default ones in my force field (a99sb-disp), but then I realized that your epsilon is ~680 kJ/mol while the default is ~3.7 kJ/mol. It feels hard to believe that the amber default is 200x too small. All the other epsilons range between 3.7 to 0.01 in my system.
Maybe I'm misinterpreting something? I'm afraid this will outweigh the subtle interactions in my peptide. Could you help ease my concerns before I use your values?
I'm looking at the nMg atom with the TIP3P-D water. And I'm looking at the parameters in the ffnonbonded.itp file for use in Gromacs.
Thanks,
-Sam
The text was updated successfully, but these errors were encountered:
I was about to substitute your sigma and epsilon values for the default ones in my force field (a99sb-disp), but then I realized that your epsilon is ~680 kJ/mol while the default is ~3.7 kJ/mol. It feels hard to believe that the amber default is 200x too small. All the other epsilons range between 3.7 to 0.01 in my system.
Maybe I'm misinterpreting something? I'm afraid this will outweigh the subtle interactions in my peptide. Could you help ease my concerns before I use your values?
I'm looking at the nMg atom with the TIP3P-D water. And I'm looking at the parameters in the ffnonbonded.itp file for use in Gromacs.
Thanks,
-Sam
The text was updated successfully, but these errors were encountered: