So, I corrected the priority order, rebuilt and tried.
Nothing has finished yet though as I am looking at a completely blank output from energy minimization with "process_m*.perl" I think there will be no difference from before.
The only thing left that I can think of is the amber version. Obviously, I can optimize my input in more than one way and try different combinations of barostat and taup settings though if nothing is moving at all, even at 40 bar and a taup of 0.1, then I don't think this tweaking the input settings will change much.
I also checked and I am up to date on patches and updates for amber18.
So, the OPC water model works just fine. However, the combination with ff19SB breaks something. Both of you managed to run the simulations, are you using amber20? If so, I suppose I will have to start asking for a license to be purchased and potentially this will solve my problems(?).
If either of you could be so kind as to look in the newly added "4 desperation/ff19SB_opc" folder and just try to run the content of "cloudJobEQ.sh" "as is", preferably as CPU run, I would be extremely grateful. To really push the boundaries here, if you manage to run the provided files "as is", could you also run the "process_m*.perl" scripts and see of you get the expected output?
You should both have read/write access to the resources so you can download/upload any files there and provide notes/feedback.
Thank you in advance and have a fantastic rest of your weekend.
Best regards
// Gustaf
________________________________
Från: Carlos Simmerling <carlos.simmerling.gmail.com>
Skickat: den 23 oktober 2020 19:28:58
Till: AMBER Mailing List
Ämne: Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP
to follow up on Dave's suggestion - I tried Gustaf's low density input
coordinate with barostat=1 + taup=0.1, and also barostat=2.
Barostat=2 gave about 5-10x increase in the slope of density vs time.
carlos
On Thu, Oct 22, 2020 at 8:48 AM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Oct 21, 2020, Carlos Simmerling 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.
>
> Carlos: have you ever tried barostat=2? It would be interesting to know
> if that makes a difference. Also, what is your starting density? If
> you use a closeness parameter of 0.7--0.8 (in solvateBox or solvateOct),
> you'll get a higher starting density, which might(?) reduce the tendency
> to get bubbles.
>
> ....dac
>
>
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Received on Sat Oct 24 2020 - 13:00:02 PDT
