[gmx-users] Help with B2AR within the POPC membrane

Aldo Segura aldosegura at gmail.com
Tue Feb 8 23:54:40 CET 2011

Dear gmxusers,

I need to perform molecular dynamics simulation of a B2AR within the
POPC membrane. I have downloaded the 128b.pdb, popc.itp and lipid.itp
files from Prof.Tieleman's group. My protein of interest is 343
residues. Also, I aligned the protein and membrane. I followed the
Justin Lemkul tutorial for KALP-15. The result of inflate.gro is in
agreement with the result showed in the tutorial (Visual inspection
with VMD). However, the result of the first minimization shows that
the protein and lipids are separated rather than starting to pack. I'm
using gromacs-4.5.3.

Can someone help me?

my minim.mdp file:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
define		= -DSTRONG_POSRES ; position restrain the protein
integrator	= steep		; Algorithm (steep = steepest descent minimization)
emtol		= 1000.0  	; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps		= 50000	  	; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist		= 1		; Frequency to update the neighbor list and long range forces
ns_type		= grid		; Method to determine neighbor list (simple, grid)
rlist		= 1.2		; Cut-off for making neighbor list (short range forces)
coulombtype	= PME		; Treatment of long range electrostatic interactions
rcoulomb	= 1.2		; Short-range electrostatic cut-off
rvdw		= 1.2		; Short-range Van der Waals cut-off
pbc		= xyz 		; Periodic Boundary Conditions (yes/no)

Best regards,

Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegurac at ipn.mx; aldosegura at gmail.com

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