[gmx-users] [ pairs_nb ] directive problems

[Mark Abraham]

Hi,

Thanks for the good description of the problem!

It does look like [ pairs_nb ] is incompletely supported in grompp - that's
what that error message says. I would speculate that this has never worked
since Berk introduced it in 2008, to replace an old implementation of
[pairs] type 3. This can be fixed, but I don't have any inputs that
actually use the new code. Are you able to help check whether a fix works
as you expect, please?

Mark

On Thu, May 28, 2015 at 11:01 AM João Martins <joaomartins139 at gmail.com>
wrote:

> Hi everyone,
>
> I'm trying to use the pairs_nb directive in order to decouple charge and
> VDW interactions of a small ligand in water but I'm running into problems
> with the implementation and understanding the manual. I know I could be
> using the couple-moltype and couple-intramol commands in my mdp file, but
> in my binding decoupling step those are not possible as I have my ligand
> and protein itps merged and as so I'm trying pairs_nb on a simpler system.
>
> On the manual's table 5.5 the directive takes qi, qj (e); V**; W**. Using
> the combination rule 1 I've manually combined the LJ parameters for all
> pairs present in the ligand itp [ pairs ] directive and placed them in the
> [ pairs_nb ] section like so:
>
> ...
> [ pairs ]
>
> [ pairs_nb ]
>     1     4     1  -0.3500 -0.2840 0.358141285 0.2343
>     1     7     1  -0.3500 -0.3910 0.358141285 0.2343
>     1    10     1  -0.3500 -0.3910 0.358141285 0.2343
>     1    18     1  -0.3500 0.0900 0.298451071 0.185231995
>     1    19     1  -0.3500 0.0900 0.298451071 0.185231995
>     2     5     1  -0.2840 -0.3500 0.358141285 0.2343
> ...
>
> One would believe this agrees with the manual, as it has, for line 1:
>
> atom number 1; atom number 2; function type; charge atom 1; charge atom 2;
> combined sigma; combined epsilon
>
> However, I get this error when using it:
>
> Software inconsistency error:
> unknown directive
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I've been able before to at least force intramolecular VDW interactions to
> be kept throughout the decoupling steps by using the [ nonbond_params ] for
> both state A and state B atom types, but since my goal here was to also
> decouple instead of annihilating the intramolecular charge interactions,
> I'm playing around with the [ pairs_nb ] directive.
>
> Anyone with more experience than me using this can please tell me what I am
> doing wrong?
>
> Best regards,
> João
>
>
> *Joao Martins*
>
> joaomartins139 at gmail.com
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