----- Original Message ----- From: Thanasis Koukoulas <[email protected]> Date: Thursday, June 3, 2010 23:26 Subject: [gmx-users] extra non bonded interaction To: [email protected]
----------------------------------------------------------- | > hello > > I have a problem with C10O3H. The problem is that i use Trappe model and > there you can add an extra repulsive interaction of molecule 10 (Oxygen) with > molecule 14 (Hydrogen). The formula that TraPPE uses is 4E7/rij^12. with the > transformation of 4E7in gromacs units (kJ*nm^12*mol-1) i take a numper > 3.325789e-7 witch until now i put it in [pairs] with the sexond function like > this: > > [Pairs] > 10 14 2 0 0 0 03.325789e-7 This line doesn't seem to have enough fields (See table 5.4 of manual) > the zeros i use is for fudgeQQ because i dont want to have coulomb 14 in > this pair and charges of both of them for the same reason. it seem to work > because at the end i have a coulombic energy 1-4 at a reasonable price but > the total energy is not correct. Construct a toy example (minimal single molecule in vacuo?) that will let you trouble-shoot what you are doing by computing by hand what the energy should be. Compare with GROMACS with and without this extra [pairs]. Be sure your combination rule paradigm is what you want it to be. Mark > please if someone can think smth answer me. The prices i get i can compare > them with another researcher who did the same work with the use of monte > carlo. i am stucked for three months and i have read th manual over and and > over again without result.... | -----------------------------------------------------------
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