[gmx-users] About membrane protein

Justin Lemkul jalemkul at vt.edu
Mon Jan 13 23:51:00 CET 2014

On 1/13/14, 5:13 PM, paulxie wrote:
> Hi everyone,
> I am doing a simulation of lipid bilayer and membrane protein following the
> tutorial on the VT webpage. Everything is fine except  the generated

Are you using the tutorial system, or are you applying the tutorial's procedure 
to some other membrane protein system?

> confout.gro after I ran energy minimization (mdrun -deffnm confout -nt 1).
> The inserted membrane protein (transmembrane helix + extra-cellular domain)
> totally came out of the lipid bilayer. Have anyone met this before? Thanks!

The simple answer is that you built the system incorrectly.  The better answer 
depends on the answer to the question above.



Justin A. Lemkul, Ph.D.
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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