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

[Justin Lemkul]

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

==================================================