what is your pressure coupling constant? I often get vacuum bubbles unless
I include a step in my equilibration with tight coupling, taup around 0.1
or smaller.
On Wed, Oct 21, 2020 at 8:37 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> 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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Received on Wed Oct 21 2020 - 07:00:02 PDT
