[gmx-users] [ pairs_nb ] directive problems

João Martins joaomartins139 at gmail.com
Thu May 28 11:00:45 CEST 2015

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,

*Joao Martins*

joaomartins139 at gmail.com

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