[gmx-users] defining parameters in a separate itp file

[Dave M]

Hi Justin,

Thanks, not sure [distance_restraints] also does not work for me. Though
pull code works (like shared by other user Mustafa in recent discussions).

My top files contain this:
[ intermolecular_interactions ]


[ distance_restraints ]

; ai aj type index type’ low up1 up2 fac

  1  155  1    0     1     0.0 0.3 0.4 1.0


I get this error:

NMR distance restraints with multiple copies of the same molecule are

currently only supported with ensemble averaging. If you just want to
restrain

distances between atom pairs using a flat-bottomed potential, use a
restraint

potential (bonds type 10) instead.

I do not have multiple copies of the same molecule (except water
molecules!) and the atom numbers here belong to two different molecules. I
also tried using type' = 2 but still error remains the same. Would have
been great if distance_restraints work as it seems to be bit cleaner way
than modifying a pull code. I want to keep number of small molecules near
to a rod like bigger molecule; just like beads on a string. So
distance_restraints or something similar will be great.

Dave

On Tue, Oct 29, 2019 at 5:45 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/28/19 6:21 PM, Dave M wrote:
> > Hi Justin,
> >
> > Thanks for your reply but am getting error suggesting a intermolecular
> > chemical bond is not allowed:
> >
> > Program:     gmx grompp, version 2016.4
> >
> > Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649)
> >
> > Fatal error:
> >
> > The intermolecular_interaction can not contain chemically bonding
> > interactions
> >
> > [ molecules ]
> >
> > ; name        number
> >
> > molA 1
> >
> > molB 1
> >
> > W  2420
> >
> >
> > [intermolecular_interactions]
> >
> >   [ bonds ]
> >
> >      1     158     1  0.4  2000
> >
> > This is coarse-grained model and as a simple test I used global atom
> > numbers between two water single particles (intermolecular) but I get the
> > same error.
>
> In that case, use a [distance_restraints] directive under
> [intermolecular_interactions] (though this will limit your domain
> decomposition setup) or use the pull code to maintain a restraint rather
> than messing with the topology.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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