There is still some empty space though decreasing the taup and increasing the pres0 seems to have made a dent.
I suppose I will extend the equilibration even further and keep hammering on it until it looks reasonable, it just creates a sense of unease when the system is not behaving in a “familiar” matter. Not being able to watch the “progress” with the tcl scripts is also creating som discomfort. If I cannot figure it out I suppose I can write some other script to extract time and density at least.
I also saw this flying by in leap (using default radius 1.500000 for EPW). I suppose that could be a cause of the unmentioned “warnings” in leap though this should only affect i atom per water and I am seeing 21000 not printed warnings, equal to 7000 water molecules, one thing for each atom.
However, does this have anything to do with the EPW/IOD thing mentioned in the manual? Is it recommended to loadamberParams the "frcmod.ions1lm_126_iod_opc" file when building the systems using FF19SB with OPC water?
Best regards
// Gustaf
> On 22 Oct 2020, at 09:10, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Hello Carlos
>
> I am trying a run with tap 0.1 to see what happens. I am just surprised as the other two systems using ff14SB and spce or tip3p water equilibrates as expected.
>
> I am also puzzled as to why the “process_min" and “process_md" scripts fail to extract data from energy minimisation and pressure equilibration for the ff19sb/opc system and not for the ff14sb/spce/tip3p systems, while working for extracting temperature data.
>
> I realised that I am setting up the systems using amber/ambertools20 while running the simulations on amber18. Still, there are no reported errors or warnings and the equilibration finished producing what seems to be normal output. Maybe there is some minor shift in the alignment of the output that I am not noticing which is causing the scripts to fail extracting the correct data.
>
> Best regards
> // Gustaf
>
>> On 21 Oct 2020, at 15:32, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>>
>> 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 Thu Oct 22 2020 - 02:00:02 PDT
