[gmx-users] No group in index file?

Xu Dong Huang xudonghmath at gmail.com
Thu Oct 31 22:03:54 CET 2013

@ 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?


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
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