[gmx-users] Simulation of membrane associated protein

[Justin Lemkul]

On 10/4/19 4:52 AM, Olga Press wrote:
> Prof. Lemkul thank you for your response.
> I'm using the output file from the charmm gui site after the MD production,
> which contain an equilibrated DOPC bilayer with TIP3 molecules  as the
> solvent (and I remove the ions before the solvation).
> I used the second option of the gmx_solvate (solvate a solute configuration)
> Do you suggest to remove the water molecule, than concatenate the protein
> coordinates with the lipids coordinates and than solvate it with water?

Yes, otherwise reposition the protein so it is further away from the 
membrane and does not lead to lipid deletion.

-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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