> On 24 Oct 2020, at 21:58, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Mon Oct 26 2020 - 01:00:02 PDT
