[gmx-users] [ pairs_nb ] directive problems

[João Martins]

Ok, thanks, will do.

Cheers,
João



*Joao Martins*

joaomartins139 at gmail.com

On Fri, May 29, 2015 at 12:14 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi Joao,
>
> That's great. You can find my guess at a fixed version, based on the 5.0
> bugfix branch, at https://gerrit.gromacs.org/#/c/4666/. There's a download
> link there, where you can get the putative fix in any format that suits
> you, e.g. various tarballs. You can build and install that in the usual
> way. Do let us know how you go, here or off-list as appropriate!
>
> Mark
>
> On Fri, May 29, 2015 at 11:19 AM João Martins <joaomartins139 at gmail.com>
> wrote:
>
> > 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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