[gmx-users] URGENT query regarding pbc = no in grompp in membrane simulations

[Antara mazumdar]

i want to simulate a system having membrane and proteins with pbc=no to
allow surface effects. I use the following settings in my production mdp
file :

 Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 100000000     ; 2 * 100000000 = 2 ms
dt              = 0.002         ; 2 fs
; Output control
;trr file
nstxout         = 500000        ; save coordinates every 1ns
nstvout         = 500000        ; save velocities every 1ns
nstenergy       = 10000         ; save energies every 20ps
nstlog          = 10000         ; update log file every 20ps
;xtc file
nstxtcout       = 10000         ; xtc compressed trajectory output every 20
ps
; Bond parameters
constraint_algorithm   = LINCS    ; holonomic constraints
constraints    =       none


;ns-type                = simple
nstlist                 = 0
rlist                   = 0
coulombtype             = Cut-off
rcoulomb                = 0.0
rvdw                    = 0

Periodic boundary conditions
pbc                 = no                ; 3-D PBC
; Velocity generation
gen_vel         = YES   ; Velocity generation is on
comm_mode      = ANGULAR


​however i get LINCS warning and also the log file says this :

​Your simulation settings would have triggered the efficient all-vs-all
kernels in GROMACS 4.5, but these have not been implemented in GROMACS
4.6. Also, we can't use the accelerated SIMD kernels here because
of an unfixed bug. The reference C kernels are correct, though, so
we are proceeding by disabling all CPU architecture-specific
(e.g. SSE2/SSE4/AVX) routines. If performance is important, please
use GROMACS 4.5.7 or try cutoff-scheme = Verlet.

kindly suggest something ..

-- 
Best
*,*
Antara

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Systems Biology Group
CSIR - Institute of Genomics & Integrative Biology
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