Re: 转发：[gmx-users] gromacs on GPU
mark.j.abraham at gmail.com
Sun Jun 23 21:39:50 CEST 2013
On Sun, Jun 23, 2013 at 3:30 PM, <sunyeping at aliyun.com> wrote:
> Dear gromcas users,
> Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, the following is a mdp file which runs well on cpu, but when I add the option "-testverlet" to mdrun in order to run it on GPU, it returns error "Fatal error:User non-bonded potentials are not (yet) supported with the Verlet schemeFor more information and tips for troubleshooting".
Thanks, I can now use a copy-paste to see that this message should not
be generated by your .mdp file below. I have filed a bug report
http://redmine.gromacs.org/issues/1289. In the meantime, I suggest you
use normal PME. FYI, there is an ongoing debate elsewhere on Redmine
that PME-Switch might be a bad idea anyway...
Next time you post an .mdp file please make the line wrapping readable.
> Could you check the mdp file for me to see how to modefy it to make it suitable to GPU? Thanks in advance!
> integrator = mdnsteps = 50000000dt = 0.002constraints = all-bondsnstcomm = 100ns_type = gridrlist = 1.2rcoulomb = 1.0 rcoulomb-switch = 0.9 rvdw =1.0vdwtype = shiftrvdw-switch = 0.9coulombtype = PME-Switch;Tcoupl = v-rescaletau_t = 0.1 0.1tc-grps = protein non-proteinref_t = 300 300Pcoupl = parrinello-rahmanPcoupltype = isotropictau_p = 0.5compressibility = 4.5e-5ref_p = 1.0gen_vel = nogen_temp = 310gen_seed = -1nstxout = 500nstenergy = 100energygrps = chA chClincs-iter = 2DispCorr = EnerPresoptimize_fft = yes
> Yeping Sun
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