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

[Dave M]

Hi Justin,

Will appreciate any suggestions about the error am getting with
distance_restraints.
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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>