[gmx-users] No group in index file?
jalemkul at vt.edu
Thu Oct 31 22:17:47 CET 2013
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
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.
> 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 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.
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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