[gmx-users] Problem with OpenMP+MPI

[Justin Lemkul]

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

-- 
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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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