Hi all. I think I'm having a really strange problem:
Well, I have some simulations being performed, and wanted to remove from the bigger molecules any vdw or coulombic intramolecular interaction "longer" than 1-4. So, from 1-5 included forward, I would like to remove from the energetic calculations, but not from the interaction dynamics. To do so, I've performed the simulation with nexcl = 3 (standard, and which would include them in the dynamics), and after I increased this number and performed a mdrun -rerun "ressimulation". Then, I runned the runedr. The problem is: I decided to make a test run. I expect that a "nexcl" number bigger than the total should not yeld problems. So I choosen to increase the nexcl in C2F6 from the standard 3 to 4. Then I runned runedr in both results, and got the following: nexcl = 3: Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Bond 3040.69 70.0697 66.5161 0.381591 76.3189 Angle 4220.72 79.1057 78.0402 -0.224121 - 44.8247 Ryckaert-Bell. 22594.3 0.369332 0.369284 0.000103437 0.0206876 LJ-14 4345.47 44.7911 44.5899 -0.0734496 - 14.6901 Coulomb-14 26656.3 12.5831 12.5831 0.000785301 0.157062 LJ (SR) -7476.61 69.8678 69.7072 -0.0820061 - 16.4014 Disper. corr. -233.013 1.80332 1.80306 -0.000532475 - 0.106496 Coulomb (SR) 202.088 3.63903 3.62648 -0.00522946 - 1.0459 Coul. recip. -228.367 1.4159 1.40872 0.00246637 0.49328 nexcl = 4: Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Bond 312.923 891.374 891.099 0.383169 76.6345 Angle 425.523 1210.88 1210.81 -0.224334 - 44.8673 Ryckaert-Bell. 2259.64 6430.13 6430.13 8.98693e-05 0.017974 LJ-14 434.682 1236.91 1236.9 -0.073917 - 14.7835 Coulomb-14 2665.87 7586.12 7586.12 0.000608334 0.121668 LJ (SR) -747.691 2127.89 2127.89 -0.0822151 - 16.4432 Disper. corr. -23.3034 66.3157 66.3157 -0.000532475 - 0.106496 Coulomb (SR) 20.2105 57.5108 57.5101 -0.00521119 - 1.04225 Coul. recip. -22.8387 64.9888 64.9886 0.00246332 0.492669 And the results, for me, doen't make sense. First, all the contributions, *including* bonds, angles and dihedralss that are *not* to be affected by the nexcl, are reduced by almost 10. Second, since we are talking about C2F6, which doesn't have any atom farthen than 3 bonds from any other, neither the vdw and coulombic contibutions should have been affected. Could please someone help me with this matter? What have I missed in the logics here? Thanks a lot for everybody in advance! Sincerally yours, Jones
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