Moeed wrote:
Hello,
I am compressing a single extended PE chain (16 nm in length) in a box
of 20nm in vacuo to get a more realistic shape of the polymer. Although
system is small (only 362 atoms), whatever -np # I choose simulation
runs very slowly. Is that because of the presence of voids? Is there a
way to speed up the runs? I have no clue on this. Thanks!
PME in vacuo is both extremely slow and unnecessary. Proper vacuum treatment is
a non-periodic system with infinite cutoffs (i.e. rlist=rvdw=rcoulomb=0). You
shouldn't have to compress this system to get it into a reasonable
configuration. The simulations should run extremely fast for such a small
amount of atoms, allowing you to obtain a nice, long, converged trajectory.
-Justin
(mpirun -np 4 mdrun_mpi ....... -pd)
starting mdrun 'Polymer'
1000000 steps, 2000.0 ps.
step 0
step 100, will finish Thu Mar 24 19:33:34 2011
step 200, will finish Thu Mar 24 19:29:18 2011
step 300, will finish Thu Mar 24 19:27:42 2011
step 400, will finish Thu Mar 24 19:27:13 2011
step 500, will finish Thu Mar 24 19:27:54 2011
pbc = xyz
; Run control
integrator = md
dt = 0.002
nsteps = 1000000 ;5000
nstcomm = 100
; Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
; Neighbor searching
nstlist = 10
ns_type = grid
; Electrostatics/VdW
coulombtype = PME
vdw-type = Shift
rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
; Cut-offs
rlist = 1.25
rcoulomb = 1.25 ;1.1
rvdw = 1.0
; PME parameters
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
;optimize_fft = yes
; Temperature coupling
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = berendsen;Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 0.5 0.5
compressibility = 4.5e-5 4.5e-5
ref_p = 10 10
; Velocity generation
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = none;all-bonds
constraint-algorithm = lincs
--
========================================
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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