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

[Tsjerk Wassenaar]

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.mazumdar at 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          = 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
> South Campus, New Delhi-110020
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-- 
Tsjerk A. Wassenaar, Ph.D.