[gmx-users] No group in index file?

[Justin Lemkul]

On 10/31/13 5:03 PM, Xu Dong Huang wrote:
> @ Justin,
>
> Excellent advice. Thank you! And for the equilibrium angle, what is the
> approximate range I can define it to be? Say target is 90 degrees, should I
> define maybe 130 and let it oscillate? I guess question is how far is too far
> off?
>

This is what I meant about a predefined outcome.  If you set the equilibrium 
value of the angle at 130 degrees, you're going to get a distribution centered 
at 130 degrees.  The odds of it sampling any configurations at 90 degrees are a 
function of the force constant, but still would be rare, so this approach makes 
no sense to me (there is a huge difference between 90 and 130).  If the target 
is 90, set it for 90.  Tune the force constant to match the distribution.

-Justin

> Thanks,
>
> On Oct 31, 2013, at 4:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/31/13 4:44 PM, Xu Dong Huang wrote:
>>> @ Justin,
>>>
>>> I did not define [angles] in the topology but I do have the angles
>>> result from All-atom run using OPLS forcefield. The reason for me not to
>>> include it in MARTINI forcefield topology is because I wanted to see if
>>> it will produce similar angle result of atom 1&2, 1&3 and 2&3 in martini
>>> water since the behavior of particle types I chose for my 3 atoms are
>>> well defined by martini at this point. My interest is to find for which
>>> force constant K value will the martini model match the all-atom model
>>> using OPLS.
>>>
>>> And you’re right, sorry, I got confused about the angles, there should
>>> only be 1. However, even the angle value I received doesn’t match the
>>> traditional all-atom result.
>>>
>>> What will happen if I define the [angles] part with the angles I
>>> received from traditional simulation? Because ultimately I am trying to
>>> find the k value parameter that will make the 3 particle display an angle
>>> similar to traditional run.
>>>
>>
>> If you define an equilibrium angle for 1-2-3, it will oscillate
>> harmonically around that value, with the distribution determined by the
>> value of k.  I suspect that is how you can tune the parameters, by matching
>> the distributions produced in the two simulations rather than a single
>> target value, because with the angle defined in the topology, you're sort
>> of predetermining the outcome.
>>
>> -Justin
>>
>> -- ==================================================
>>
>> Justin A. Lemkul, Ph.D. Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences School of Pharmacy Health Sciences
>> Facility II, Room 601 University of Maryland, Baltimore 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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