Hello Amber Community,
The molecular system that I typically simulated in my research consisted of 1000 water and 1000 butanol molecules, and the results were accurate. I expanded the system to include 10,000 water and 500 2-butanol molecules (a total of 37,500 molecules). The results were satisfactory. However, when I attempted RDF analysis for butanol and water with a 0.01 Å bin size and a 20 Å distance, (radial H_O_rdf 0.01 20 :WAT.H* :WAT.O volume)I obtained the RDF for butanol but not for water. It is possible that the absence of water RDF files is due to the large number of atoms. I also observed some unusual coordinates in the .nc, .mdcrd, and PDB files for a single configuration. The box size of the system is approximately 74 Å x 75 Å x 74 Å, and we expect the coordinates of the molecules to fall within this range. It appears that handling a system of this size may have presented challenges. I would appreciate guidance on the best approach to simulate the system and obtain the RDF for 10,000 water molecules.
Cpptraj Generated trajectory
-416.730-101.326 -63.637-416.090-100.840 -62.850-416.804-100.678 -64.539-416.217
-102.181 -64.139-418.185-101.675 -63.175-418.079-102.236 -62.258-418.574-102.283
-63.949-419.059-100.475 -62.950-418.942 -99.856 -63.824-418.632 -99.829 -61.775
-417.848 -99.261 -61.895-420.581-100.802 -62.843-420.865-100.998 -61.806-421.155
-99.857 -62.993-420.970-101.527 -63.589 -50.998 -82.641 809.933 -51.440 -83.007
808.977 -51.467 -81.702 809.972 -51.498 -83.283 810.656 -49.496 -82.612 810.096
-49.449 -82.708 811.137 -49.052 -81.690 809.754 -48.701 -83.737 809.502 -47.635
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Received on Thu Nov 09 2023 - 22:30:02 PST
