Hello, I'm trying to fill a box with methanol using CHARMM FF Parameters. I also need to do this for ethanol and 1-propanol.
For ethanol, each individual molecule had approximately -19 kJ/mol of potential energy, then I placed 1000 in a box, performed nvt, npt, etc. End Result: A negative potential energy (it means that its stable?) and a density of 0.785 g/cm3 compared to actual 0.789 g/cm3 at 1 atm, 298 K. This result seemed ok. For methanol and 1-propanol, each individual molecule had a larger 24 - 64 kJ/mol respectively, due to Coulomb 1,4 pair interactions (for example, for methanol between the HA 0.09 and the H 0.43 gives a large 64 kJ/mol). Again placed 1000 each in 2 separate boxes, performed nvt,npt,etc on each one. End Result: A still positive potential energy for each box (shouldn't this be negative after running npt? on both) and a density that was 0.789 g/cm3 (for 1-propanol)compared to actual 0.803 g/cm3 1-propanol at 1 atm, 298 K. Methanol density a bit closer 0.787 compared to 0.791 g/cm3. My questions are: -There should definetly be a positive potential energy after running npt, correct? Otherwise it wouldn't be stable? I understand that the 1,4 coulomb interactions should cancel out with nearby molecules. *For CHARMM, they state that unless otherwise 1,4 parameters exist already, they use a full scale 1.0 of the regular LJ, coulomb potential. -As for the density, I know it's somewhat close but I'm trying to be as accurate as possible. I read somewhere that the average cut-off (rlist) is usually 1.4 for CHARMM and I had mine set to 1. I'm guessing that having a larger cutoff would contribute more molecules to the LJ, coulomb which might rise the density a bit to the correct value? I'm still new to Gromacs so I appreciate all of anybodys help. Thanks a bunch. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com
minim.mdp
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nvt.mdp
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npt.mdp
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ethanol.itp
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methanol.itp
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1propanol.itp
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