I am run a series of simulation comparing ff14SB-SPCE, -TIP3P and ff19SB-OPC.
- First regarding OPC and LEaP
While preparing the ff19SB-OPC system I get a warning for every atom molecule in the system. However, there is no warning printed. Even increasing the verbosity level to 2 I see no details regarding what LEaP is warning about when considering OPC water. Everything finishes without errors in the end though I find it worrying that there is no information regarding the warnings printed. I have done this with a “general” WAT pub file setting WAT=OPC and building the box using OPC pdb file, the outcome is the same in both cases.
- Second, regarding preformed simulations
+ While evaluating the equilibration I noticed something rather strange. When running process_*out.perl scripts. Checking the temperature equilibration using the process_mdout.perl script produces the expected data, everything looks good.
+ However, checking the energy minimisation, the process_minout.perl script produces completely empty output files.
+ Furthermore, checking the pressure equilibration, looking at the summary.DENSITY using the process_mdout.perl script only produces the time column and no data column (density)
The output files contain all the values expected, I cannot se any difference in formatting between the ff19SB system and the ff14SB systems, everything aligns, values all differ though look reasonable. What am I missing here?
Best regards
// Gustaf
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Received on Wed Oct 21 2020 - 01:30:02 PDT
