[gmx-users] error about g_bar
jalemkul at vt.edu
Mon Aug 18 03:30:30 CEST 2014
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
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
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