[gmx-users] Problem with OpenMP+MPI

[jesmin jahan]

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??

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?

Thanks,
Jesmin
On Wed, Feb 27, 2013 at 10:33 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/27/13 10:25 AM, jesmin jahan wrote:
>>
>> Thanks Justin.
>> Well, I am felling stupid now! Could you kindly provide me some better
>> .mdp parameters that make more sense?
>>
>> gromacs 4.6 gives me error with my previous parameters which were
>> working perfect in gromacs 4.5.3
>>
>> It says we have to use cut-off verlet, either we have to use coupling
>> temp or we have to set verlet-buffer-drift = -1.
>> Then it says set pbc to xyz or xy. I tried to change my rlist or other
>> cutoff values. It says box is too large or small.
>>
>> So, i am really very confused!
>> It will be very kind of you, if you can suggest me some parameters
>> which match best with my previous parameters namely:
>>
>>
>>>> constraints         =  none
>>>> integrator          =  md
>>>> pbc                 =  no
>>>> dt                  =  0.001
>>>> nsteps              =  0
>>>> rcoulomb            = 300
>>>> rvdw                = 300
>>>> rlist               = 300
>>>> nstgbradii          = 300
>>>> rgbradii            = 300
>>>> implicit_solvent    =  GBSA
>>>> gb_algorithm        =  HCT ;
>>>> sa_algorithm        =  None
>>>> gb_dielectric_offset    = 0.02
>>>>
>>>> optimize_fft             = yes
>>>> energygrps               = protein
>>
>> -----------------------------
>>
>
> For implicit runs, I always set:
>
> pbc = no
> ns_type = simple
> comm-mode = angular
> rlist = 0
> rcoulomb = 0
> rvdw = 0
> nstlist = 0
> rgbradii = 0
> nstgbradii = 1
> coulombtype = cutoff
> vdwtype = cutoff
>
>
> -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
>
> ========================================
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-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.