[gmx-users] Constraints of distance

[Justin Lemkul]

On 6/11/13 3:47 PM, Steven Neumann wrote:
> Thank you Justin. So using nrexcl 0 or 1 (should be the same with
> constraints) and type 1 will allow bonded atoms to interact (vdW) with each
> other?
>

No, there will be differences for type 1 in this case.  Type 1 generates 
exclusions per nrexcl.  Using nrexcl = 0 will allow for all nonbonded 
interactions to be calculated, but nrexcl = 1 will exclude interactions with 
neighboring particles.  So the combination of nrexcl = 0 with type 1 
constraints, or any value of nrexcl with type 2 constraints will allow for all 
nonbonded interactions to be calculated.

-Justin

>
> On Tue, Jun 11, 2013 at 6:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/11/13 10:46 AM, Steven Neumann wrote:
>>
>>> I was not sure about the fucntion type (1 or 2). Once in manual it is
>>> stated that function 1 is only for exclusions and another time it can be
>>> used to miimc bonds. Both functions are working though.  Thanks anyway.
>>>
>>>
>> More precisely, constraints of type 1 generate exclusions between bonded
>> atoms within nrexcl (defined in the topology), whereas type 2 do not.
>>   Whether or not you need the constraints to do this depends on the nature
>> of the force field.
>>
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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