[gmx-users] mdp file coarse grained simulation with cutoff-scheme =?utf-8?Q?=3D_?=Verlet

[Carlos Navarro Retamal]

Dear Mark,
Thanks for your quick reply.
I used this one as a template (provided by one of the tutorials of martini)



> dt = 0.02 nsteps = 1000000 nstxout = 0 nstvout = 0 nstlog = 10000 nstxtcout = 1000 xtc-precision = 10 rlist = 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein W tau-t = 1.0 1.0 ref-t = 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau-p = 12.0 compressibility = 3e-4 ref-p = 1.0 refcoord_scaling = all
>  
>  
>  
>  

and i add cutoff-scheme = Verlet, but i got the following errors:

> ERROR 1 [file dynamic.mdp]:
>   With Verlet lists only cut-off LJ interactions are supported
>  
>  
> ERROR 2 [file dynamic.mdp]:
>   With Verlet lists only cut-off, reaction-field, PME and Ewald
>   electrostatics are supported



so my question is. For a system consisting in a protein and a membrane, which options are the correct ones for the vdw and the electrostatic interactions? I read on another topic that for the electrostatic interactions the PME approximation is the best, but i don’t know which one would be the best for the vdw term.
Kind regards,
Carlos

--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl


On Sunday, December 14, 2014 at 3:58 PM, Mark Abraham wrote:

> Hi,
>  
> In one sense, there's nothing to do. Set the cut-off scheme to Verlet, and
> choose your non-bonded and/or integrator setup according to the
> recommendations for your model physics. mdrun's job is to implement it
> faithfully, but it's your job to choose it ;-)
>  
> Mark
>  
> On Sun, Dec 14, 2014 at 7:41 PM, Carlos Navarro Retamal <cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)>
> wrote:
> >  
> >  
> > Dear gromacs users,
> > I’mt trying to improve the performance of some CG simulations by using GPU
> > (with cutoff-scheme = Verlet). So i’m trying to create an specific mdp file
> > for my simulations (4.6.3 version for now) without luck so far.
> > Could someone provide me a parameters file? i'll be appreciated for your
> > help.
> > Have a nice day,
> > Carlos
> > --
> > Carlos Navarro Retamal
> > Bioinformatic engineer
> > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > Center of Bioinformatics and Molecular Simulations (CBSM)
> > Universidad de Talca
> > 2 Norte 685, Casilla 721, Talca - Chile
> > Teléfono: 56-71-201 798,
> > Fax: 56-71-201 561
> > Email: carlos.navarro87 at gmail.com (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
> >  
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