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

[Dave M]

Hi Justin,

I just found that using bond type 6 (instead of 1) works for my test
models. So something like this in top file works fine which is bit neat and
easier to handle for multiple molecules (compared to pull code).

[intermolecular_interactions]

 [ bonds ]

    1     158     6  0.4  1000

Just thought to reply what worked for me for future users.

Dave

On Tue, Nov 5, 2019 at 4:58 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/5/19 7:53 PM, Dave M wrote:
> > Hi Justin,
> >
> > Will appreciate any suggestions about the error am getting with
> > distance_restraints.
>
> Aside from using the pull code rather than this approach, I have no
> other suggestions.
>
> -Justin
>
> > Thanks.
> >
> > regards,
> > Dave
> >
> > On Thu, Oct 31, 2019 at 1:39 AM Dave M <dave.gromax at gmail.com> wrote:
> >
> >> 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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> >>>
>
> --
> ==================================================
>
> 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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