[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 27 16:07:14 CEST 2012

On 4/27/12 10:00 AM, Bala S wrote:
> Anirban,
> Exactly.. That's the gap (either side of the leaflets) I was mentioning
> about. I'll try EM and check itagain.

EM won't fill in solvent gaps.  If you're using my protocol for increasing the C 
radius in vdwradii.dat, then a small gap is normal and will close when doing 
equilibration as the solvent fills in around the lipid headgroups.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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