[gmx-users] mdp file coarse grained simulation with cutoff-scheme = Verlet

[Mark Abraham]

On Sun, Dec 14, 2014 at 8:11 PM, Carlos Navarro Retamal <cnavarro at utalca.cl>
wrote:
>
> Dear Mark,
> Thanks for your quick reply.
> I used this one as a template (provided by one of the tutorials of martini)
>

Tutorials are generally not normative. Some people's tutorials are
deliberately cut down so that they run quickly. Read the real literature
from the authors of the force field - both the original work and the things
they've published later.

> 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
>

These kinds of things are available in Gromacs 5.

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.
>

The answer to this question starts with reading the literature :-) For a
membrane system, I think PME for both Coulomb and LJ is appropriate, but
Martini was not parameterized that way, so you should follow the
parameterization they used, unless you can see they've changed their mind
later for systems relevant to yours.

Mark


> 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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