[gmx-users] Problem with OpenMP+MPI

[Justin Lemkul]

On 2/27/13 10:54 AM, jesmin jahan wrote:
> Many thanks to you Justin for your help.
>
> Now my .mdp file looks like:
>
> constraints         =  none
> integrator          =  md
>
> pbc                 =  no
> verlet-buffer-drift = -1
> dt                  =  0.001
> nsteps              =  0
> ns_type             = simple
> comm-mode           = angular
> rlist               = 0
> rcoulomb            = 0
> rvdw                = 0
> nstlist             = 0
> rgbradii            = 0
> nstgbradii          = 1
> coulombtype         = cutoff
> vdwtype             = cutoff
> implicit_solvent    =  GBSA
> gb_algorithm        =  HCT ;
> sa_algorithm        =  None
> gb_dielectric_offset    = 0.02
>
> optimize_fft             = yes
> energygrps               = protein
>
> And when I run mdrun, it says
>
> "OpenMP threads have been requested with cut-off scheme Group, but
> these are only supported with cut-off scheme Verlet"
>
> Now if I add
>
> cutoff-scheme       = Verlet
>
> It says
>
>   With Verlet lists only full pbc or pbc=xy with walls is supported
>
>    With Verlet lists nstlist should be larger than 0
>
>
> So, what is the solution??
>

Use the group cutoff scheme rather than Verlet, otherwise we wind up right back 
where we were before.

> Also,  you told me
>
> "Note that implicit solvent calculations can be run on no more than 2
> processors.  You'll get a fatal error if you try to use more."
>
> Is there any documentation for this? Can I cite you if I want to add
> this information in an article?
>

It's a bug, listed on Redmine somewhere.  I doubt that requires any sort of 
citation, but if anyone asks, there are discussions in the list archive and on 
redmine.gromacs.org.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================