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Tinker: Software Tools for Molecular Design
https://dasher.wustl.edu/tinker/
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analyze issue with TIP5P #153

Closed mircodaniel closed 4 months ago

mircodaniel commented 4 months ago

When I use the tinker tool analyze with TIP5P water and particular molecule (e.g. acetic acid) I get some strange results. My .xyz file looks like this:

13 HAc_H2O 1 C 0.441909 0.390814 0.078903 209 2 3 5 2 O 1.548455 0.693361 -0.351452 210 1 3 O -0.165194 1.060171 1.090898 211 1 4 4 H 0.403730 1.758478 1.373750 212 3 5 C -0.400224 -0.760146 -0.448740 80 1 6 7 8 6 H -0.597172 -1.480851 0.344606 85 5 7 H -1.351979 -0.390312 -0.829515 85 5 8 H 0.120476 -1.271516 -1.258450 85 5 9 O 2.940531 0.032590 -0.026181 73 10 11 12 13 10 H 3.532313 0.352631 0.654700 74 9 11 H 3.307364 -0.812787 -0.285031 74 9 12 Lp 2.927421 0.473437 -0.569765 75 9 13 Lp 2.292372 -0.045870 0.226277 75 9

Content of .key file:

PARAMETERS "./oplsaa.prm" DIELECTRIC 1.0 NONBONDTERM ONLY OPENMP-THREADS 1

With analyze (program D for detail) I get following output:

Individual Charge-Charge Interactions :

Type Atom Names Charges Distance Energy

Charge 1-C 10-H 0.52 0.00 3.1438 13.2367 Charge 1-C 11-H 0.52 0.24 3.1292 13.2985 Charge 1-C 12-Lp 0.52 0.24 2.5701 -16.1916 Charge 1-C 13-Lp 0.52 -0.24 1.9070 -21.8217 Charge 2-O 4-H -0.44 0.45 2.3283 -14.1190 Charge 2-O 6-H -0.44 0.06 3.1330 -1.3991 Charge 2-O 7-H -0.44 0.06 3.1330 -1.3991 Charge 2-O 8-H -0.44 0.06 2.5928 -1.6905 Charge 2-O 10-H -0.44 0.00 2.2504 -15.6471 Charge 2-O 11-H -0.44 0.24 2.3166 -15.1997 Charge 2-O 12-Lp -0.44 0.24 1.4134 24.9135 Charge 2-O 13-Lp -0.44 -0.24 1.1973 29.4080 Charge 3-O 6-H -0.53 0.06 2.6833 -1.9676 Charge 3-O 7-H -0.53 0.06 2.6833 -1.9676 Charge 3-O 8-H -0.53 0.06 3.3223 -1.5892 Charge 3-O 10-H -0.53 0.00 3.7898 -11.1917 Charge 3-O 11-H -0.53 0.24 4.1785 -10.1506 Charge 3-O 12-Lp -0.53 0.24 3.5590 11.9175 Charge 3-O 13-Lp -0.53 -0.24 2.8303 14.9858 Charge 4-H 5-C 0.45 -0.18 3.2111 -4.1881 Charge 4-H 6-H 0.45 0.06 3.5432 2.5304 Charge 4-H 7-H 0.45 0.06 3.5432 2.5304 Charge 4-H 8-H 0.45 0.06 4.0236 2.2282 Charge 4-H 10-H 0.45 0.00 3.5045 10.2759 Charge 4-H 11-H 0.45 0.24 4.2183 8.5371 Charge 4-H 12-Lp 0.45 0.24 3.4348 -10.4845 Charge 4-H 13-Lp 0.45 -0.24 2.8530 -12.6227 Charge 5-C 10-H -0.18 0.00 4.2333 -3.4027 Charge 5-C 11-H -0.18 0.24 3.7116 -3.8810 Charge 5-C 12-Lp -0.18 0.24 3.5510 4.0565 Charge 5-C 13-Lp -0.18 -0.24 2.8663 5.0255 Charge 6-H 10-H 0.06 0.00 4.5288 1.0602 Charge 6-H 11-H 0.06 0.24 4.0110 1.1971 Charge 6-H 12-Lp 0.06 0.24 4.1326 -1.1619 Charge 6-H 13-Lp 0.06 -0.24 3.2284 -1.4873 Charge 7-H 10-H 0.06 0.00 5.1586 0.9308 Charge 7-H 11-H 0.06 0.24 4.7100 1.0194 Charge 7-H 12-Lp 0.06 0.24 4.3734 -1.0979 Charge 7-H 13-Lp 0.06 -0.24 3.8098 -1.2603 Charge 8-H 10-H 0.06 0.00 4.2354 1.1337 Charge 8-H 11-H 0.06 0.24 3.3637 1.4275 Charge 8-H 12-Lp 0.06 0.24 3.3761 -1.4222 Charge 8-H 13-Lp 0.06 -0.24 2.9024 -1.6544

Individual van der Waals Interactions :

Type Atom Names Minimum Actual Energy

VDW-LJ 1-C 9-O 3.8394 2.5264 16.4803 VDW-LJ 2-O 6-H 3.0534 3.1330 -0.0389 VDW-LJ 2-O 7-H 3.0534 3.1330 -0.0389 VDW-LJ 2-O 8-H 3.0534 2.5928 0.0707 VDW-LJ 2-O 9-O 3.4111 1.5749 1915.9830 VDW-LJ 3-O 6-H 3.0740 2.6833 0.0210 VDW-LJ 3-O 7-H 3.0740 2.6833 0.0210 VDW-LJ 3-O 8-H 3.0740 3.3223 -0.0308 VDW-LJ 3-O 9-O 3.4341 3.4568 -0.1647 VDW-LJ 5-C 9-O 3.7092 3.4594 -0.0750 VDW-LJ 6-H 9-O 3.1349 3.8657 -0.0338 VDW-LJ 7-H 9-O 3.1349 4.3875 -0.0172 VDW-LJ 8-H 9-O 3.1349 3.3424 -0.0622

Intermolecular Energy : 1945.8568 Kcal/mole

Total Potential Energy : 1924.8298 Kcal/mole

Energy Component Breakdown : Kcal/mole Interactions

Van der Waals 1932.1145 13 Charge-Charge -7.2847 43

As You can see there is no charge-charge interaction with 9-O and the VdW-energy of 2-O and 9-O is way too high. This happens with latest tinker version (windows version as well as linux version). It happens also when I take TIP5P water and DMP or MP, but not when I take TIP5P water and methanol.

jayponder commented 4 months ago

The issue here is not with the Tinker implementation or evaluation of the energy. Instead, I believe the problem is with your input structure. Your structure has the TIP5P oxygen and the acetic acid carbonyl oxygen at a distance of 1.5749 Ang, which is much too close. This is why you see a very large vdw interaction between those two atoms, which appears to be "correct".

Also note that there is no charge-charge interaction of any atom with the TIP5P oxygen. This is correct, as the oxygen in TIP5P has a zero charge. In the TIP5P water model, the charges are only on the hydrogen and lone pair sites.

Where did you get this input structure from?

mircodaniel commented 4 months ago

Hello Prof. Ponder, thanks a lot for the quick response. This structure is one of our program generated structures. We are trying to determine many interaction energies from different configurations. We have calculated many interactions between two molecules, but we've never observed so many configurations with that high interaction energies.

jayponder commented 4 months ago

All I can say is that the xyz structure in your first message above is not reasonable- two nonbonded oxygens cannot get as close as 1.57 Ang. Your structure should have a very high vdw energy, just as it does. So I think the problem here is not with Tinker or the OPLS-AA parameters.