[gmx-users] [ pairs_nb ] directive problems

[João Martins]

Hi Mark,

I can do that, where can I find either the fix or the fixed version?

João



*Joao Martins*

joaomartins139 at gmail.com

On Thu, May 28, 2015 at 4:11 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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