I'm sorry, actually Ray was right, I was NOT using the same AAA14.inpcrd
input file.
There's no issue here, sorry for taking your time.
On Fri, 14 Jan 2022 at 11:31, Alan <alanwilter.gmail.com> wrote:
> I've been using Conda ambertools 21.11.
>
> I'm already using a small system (NALA-ALA-CALA) and, to Ray, in my first
> email I gave all the steps for anyone to reproduce the issue, so yes, I'm
> absolutely sure I'm using the same files.
>
> With sander I do use ntmin=2 (steep descent) and maxcyc=0 so I want the
> energies at step 0 of my systems.
>
> I did suspect that python was doing 1 or more md steps so I played with md
> in mdin for sander (igb=6, imin=0, maxcyc=0, ntmin=2, nstlim=X), where I
> increased X one by one but I didn't reproduce the energies seen from
> pysander.
>
> Also, it's not SHAKE since pysander inp.ntc = inp.ntf = 1 which are the
> same as default in sander.
>
> So, I dive into the code.
>
> I'm using gitpod from https://github.com/dacase/msander
>
> Installed `sudo apt install gfortran` there.
>
> Then did:
>
> ./configure --no-rism --no-netcdf --no-boost
>
> make clean && make install
>
> Alas, it failed to build with:
>
> ...
> [MSANDER] FC extra_pts.F90
> [MSANDER] FC ../rism/amber_rism_interface.F90
> ../rism/amber_rism_interface.F90:16:6:
>
> 16 | use safemem
> | 1
> Fatal Error: Cannot open module file ‘safemem.mod’ for reading at (1): No
> such file or directory
> compilation terminated.
> make[2]: *** [Makefile:172: amber_rism_interface.API.o] Error 1
> make[1]: *** [Makefile:10: serial] Error 2
> make[1]: Leaving directory '/workspace/msander/src'
> make: *** [Makefile:4: install] Error 2
> gitpod /workspace/msander $
>
> My reasoning here was to build and compare all the original tools from
> source and in a clean, fresh, isolated machine.
>
> On Thu, 13 Jan 2022 at 17:37, David A Case <david.case.rutgers.edu> wrote:
>
>> On Thu, Jan 13, 2022, Alan wrote:
>> >In details:
>> > Python x Sander
>> >error angle : 0.48950 % 4.29874 x 4.27770
>> >error bond : 2.04820 % 0.75717 x 0.77300
>>
>> If your bond and angle energies don't agree, then debugging should be much
>> easier.
>>
>> Check things like doing a single-step minimiation instead of MD. But it
>> probably comes down to getting into the code and seeing what the python
>> gb_input is doing (in complete detail); I don't know that off the top of
>> my
>> head. It's possible that the python interface is doing somthing like
>> setting SHAKE by default, which you are not doing in your sander
>> calculation.
>>
>> You might try a very small system to see if that helps find the
>> differences.
>>
>> ...dac
>>
>>
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>>
>
>
> --
> Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
>
--
Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
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Received on Fri Jan 14 2022 - 04:00:03 PST
