Why is this urgent?
Have you tried the suggestions given by the program?
Cheers,
Tsjerk
On Wed, Jun 3, 2015 at 12:08 PM, Antara mazumdar antara.mazum...@igib.in
wrote:
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 = 1 ; 2 * 1 = 2 ms
dt = 0.002 ; 2 fs
; Output control
;trr file
nstxout = 50; save coordinates every 1ns
nstvout = 50; save velocities every 1ns
nstenergy = 1 ; save energies every 20ps
nstlog = 1 ; update log file every 20ps
;xtc file
nstxtcout = 1 ; 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
--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
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