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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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