Date: Wed, 21 Oct 2020 12:36:30 +0000
Feels like I potentially missed something entirely regarding using OPC water as I also seem to be experiencing equilibration problems. Upon visual inspection there seems to be vacuum pockets in the system which persist even after extended pressure equilibration and at highly elevated pressure.
[cid:E6D91611-3992-4A42-B37E-7D245DF0B679.client.lnu.se]
I am unsure what I might have missed. I sourced leaprc.water.opc setting WAT = OPC and built systems with only water. In addition, sourcing leaprc.protein.ff19SB and including a peptide. The system with only OPC water seems to have equilibrated nicely and I get the expected plots. I assume then that the observed behaviour must be from the included peptide.
Is there any really important thing that I am obviously missing here?
Best regards
// Gustaf
On 21 Oct 2020, at 10:10, Gustaf Olsson <gustaf.olsson.lnu.se<mailto:gustaf.olsson.lnu.se>> wrote:
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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