[gmx-users] mdp file coarse grained simulation with cutoff-scheme =?utf-8?Q?=3D_?=Verlet
Carlos Navarro Retamal
cnavarro at utalca.cl
Sun Dec 14 20:12:02 CET 2014
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.
Carlos Navarro Retamal
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:
> 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 ;-)
> On Sun, Dec 14, 2014 at 7:41 PM, Carlos Navarro Retamal <cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)>
> > 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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