Hsin-Lin Chiang wrote:
If the simulation is even stable, it will be horribly inaccurate. 12 nm cutoffs
are unheard of and 2-nm grid spacing is about 20 times too large.
Without seeing the original .mdp file that gave the high PME load, and without a
further description about how large the system is (number of atoms), it is hard
to say what you should do. Some system do not parallelize well, but I imagine
you should be able to get better performance.
-Justin
Thank you for reply
The original .mdp is below and the number of atoms is 20171
How big is the box? You don't have any vacuum space, do you? The only reason
I've seen for PME load being so large in conjunction with "normal" settings and
a simple system is if you've got a large void that causes PME to do a whole lot
of work to accomplish nothing.
-Justin
The difference is only in rlist, rcoulomb, rvdw, and fourierspacing
/title = ttt
//cpp = /lib/cpp
//constraints = hbonds
//;define = -DFLEX_SPC
/i/ntegrator = md
//emtol = 100.0
//emstep = 0.005
//dt = 0.002 ; ps !
//nsteps = 25000000 ; total 50 ns
//nstcomm = 5000
//nstxout = 5000
//nstvout = 5000
//nstfout = 5000
//nstlog = 5000
//nstenergy = 5000
//nstlist = 10
//ns_type = grid
//rlist = 1
//rcoulomb = 1
//rvdw = 1
//coulombtype = PME
//fourierspacing = 0.2
//pme_order = 6
//optimize_fft = yes
//Tcoupl = v-rescale
//tc-grps = Protein Non-Protein
//;tau_t = 0.1 0.1
//tau_t = 0.2 0.2
//ref_t = 300 300
//energygrps = A-chain B-chain SOL NA
//Pcoupl = berendsen
//Pcoupltype = isotropic
//;tau_p = 0.1
//tau_p = 0.25
//compressibility = 5.4e-5
//ref_p = 1.0
//gen_vel = yes
//gen_temp = 300
//gen_seed = 173529/
Hsin-Lin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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