is the problem now just in extracting things from the mdout file?
use of ff19SB does add a "CMAP" term to the energy output. so anything that
assumes all of the energy terms are in specific places might not work.
I imagine if you look at the file and compare to the other one you might be
able to adjust the script, or use a combination of grep and awk to extract
what you want. I don't use that perl script so can't really comment on how
flexible it is.
here is an example from a system where did MD with both force fields:
ff14SB:
NSTEP = 1000 TIME(PS) = 2101.000 TEMP(K) = 298.75 PRESS =
15.9
Etot = -44184.4117 EKtot = 10921.8008 EPtot =
-55106.2125
BOND = 442.7755 ANGLE = 1161.2657 DIHED =
1903.5578
1-4 NB = 552.1177 1-4 EEL = 4678.8785 VDWAALS =
5871.5787
EELEC = -69716.3864 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 4641.7222 VIRIAL = 4581.2633 VOLUME =
175735.8591
Density =
1.0355
------------------------------------------------------------------------------
ff19SB:
NSTEP = 1000 TIME(PS) = 3001.000 TEMP(K) = 296.65 PRESS =
58.2
Etot = -59114.2876 EKtot = 10887.3496 EPtot =
-70001.6372
BOND = 439.2101 ANGLE = 1197.8938 DIHED =
908.4324
UB = 0.0000 IMP = 0.0000 CMAP =
135.9763
1-4 NB = 560.3848 1-4 EEL = 4715.4626 VDWAALS =
7598.8540
EELEC = -85557.8511 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 4645.2896 VIRIAL = 4425.1982 VOLUME =
175073.8963
Density =
1.0436
------------------------------------------------------------------------------
On Sat, Oct 24, 2020 at 3:49 PM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat Oct 24 2020 - 13:00:02 PDT
