[gmx-users] Protein stabilization

[Justin Lemkul]

On 2/12/20 6:20 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Gromacs users,
>
>
> I'm trying to perform a protein-lipid complex simulation. While the interaction between these molecules seems reasonable, the protein Root Mean Square Deviation is too high, and I don't know how to stabilice it. Could you recommend me any simulation trick to stabilize the protein and improve the simulation?
>

If only such a magic wand existed that made our unexpected outcomes turn 
into something we want :)

If a simulation does not reproduce known behavior, something is wrong 
with the model, its preparation, the force field parameters, simulation 
is too short, etc.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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