[gmx-users] error about g_bar

[Justin Lemkul]

On 8/17/14, 10:36 AM, Swapnil Kate wrote:
> hello Justin
>
>   Thank you for your advice, that was really fruitful.
>
> can you kindly tell me how to visualize the molecule which is appearing or disappearing (lamda 0 to 1, lamda 1 to 0 respectively)?
>

Visualize it like you would anything else.  As far as the trajectory is 
concerned, there's nothing special about the (dis)appearing molecule.  The 
trajectories represent non-physical intermediates, though, so there's not much 
value in visualizing them.

> moving forward i am interested in calculating free energy of reacting mixtures so could you please tell me how to make a files and how to move forward?
>

You can't simulate chemical reactions with classical MD.  If there is something 
more specific you need information about, please ask a focused question with 
specific details.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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