[gmx-users] Could you help me deal with GC-AdResS approach implemented in Gromacs?

[John Whittaker]

Hi Ekatherina,

I currently develop AdResS (I am the successor to the post-doc who
uploaded the files to the e-cam site) and would be happy to help, but
since Gromacs no longer supports AdResS, perhaps we should continue the
conversation off the user list. If you'd like to talk about the method or
some more advanced applications, shoot me an email
(johnwhittake at zedat.fu-berlin.de).

For posterity's sake, though, just to answer your questions and comment on
some things here:

> I downloaded and installed Gromacs 5.1.5. (I understand that
> GC-AdResS is implemented in this version).

Correct, but as you note below, the vanilla Gromacs 5.1.5 distribution
implements the AdResS version with a switching function, not the "abrupt"
coupling version that is used in
(https://www.researchgate.net/publication/326361115_Adaptive_resolution_molecular_dynamics_technique_Down_to_the_essential).
Regardless, it should work.

> There is a folder (folder attached) for a test run on the site
> (https://e-cam.readthedocs.io/en/latest/Meso-Multi-Scale-Modelling-Modules/modules/GC-AdResS/Abrupt_AdResS/readme.html).
> When I tried to launch, I got the following error:
> Program gmx grompp, VERSION 5.1.5
> Source code file:
> /........./gromacs-5.1.5/src/gromacs/gmxpreprocess/readir.c, line: 2690
> Fatal error:
> 13824 atoms are not part of any of the T-Coupling groups
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I had a number of questions:
> 1) How can I solve this problem?

Hmmm, it looks like the person who uploaded the example files created his
index file incorrectly.

- First, delete index.ndx
- create a new index file (gmx make_ndx -f conf.gro)
   - enter "a WCG"
   - enter "!a WCG"
   - enter "name 4 EXW"
   - now quit
- The index file should now be correct

There were a couple issues but namely, he created a group for the explicit
water atoms in the index file by choosing the complement of the WCG set
(e.g., !WCG), but accidentally did not change the group name to EXW.

> 2) Will the smooth GC-address work by default there?

I just tested it and it will *work*, but the results won't really make
sense. A number of the parameters were created using the abrupt method, so
they should only be used with the abrupt patch.

> 3) Does it matter that I did not register the existing Source Code
> (patch file for Abrupt GC-Address) anywhere?

Apply the patch. It makes the code faster and it makes the most sense for
the example case given.

I apologize for the difficulty... It seems there wasn't much care taken in
uploading and outlining the materials on the e-cam website.

The AdResS method has gone through many changes since it was last
supported in Gromacs, and things can get very complicated without a guide.
Again, let me know if you would like more help or to talk about AdResS.

Best,

John

> --
> Sincerely,
> Ekatherina
> oeg at isc-ras.ru
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