Hi all,
I'm running some free energy calculations (in vacuo and in solution) for a set
of molecules I am trying to parameterize. All the molecules are fairly small,
about 30-35 atoms in each. The solvated calculations go smoothly, and rather
quickly (~5 hr/ns on two nodes). I am running into a problem when I do the in
vacuo calculations. Since I am constraining all bonds, I am running things on
a local machine in the lab (single core AMD64 Opteron). I get as far as NVT
equilibration (removing charges only) before I give up and kill it, since it
takes so long. A 10-ps NVT run takes about 20 minutes, but that adds up to
over 5 days for my 5-ns production run! The machine is no slouch; I have used
it to run other small NVT/NPT/MD runs with good performance. I get similar
performance on another machine that is even faster (a single CPU of the 2-CPU
node on our supercomputer). The installations of Gromacs on both are fine, as
far as I can tell, and both have been used extensively.
I am using Gromacs version 3.3.3, and I have attached my .mdp file and the tail
end of my log file for reference. If anyone notices anything obvious that I'm
doing wrong, I would be grateful if you pointed it out! I see in the log of
the slow run (in vacuo) that the 3D-FFT calculation is dominating the CPU
usage. Is that indicative of any problem?
Thanks for your attention.
-Justin
---My nvt.mdp file---
; NVT equilibration for free energy calculation
title = 10-ps NVT equilibration for free energy calculation
cpp = /usr/bin/cpp
include = -I/home/jalemkul/Gromacs/Free_Energy/Topologies/
; Run control parameters
integrator = sd
; start time and timestep in ps
tinit = 0
dt = 0.002 ; 0.002 ps = 2 fs
nsteps = 5000 ; 10 ps total
; COM motion removal
nstcomm = 100
; Output frequency
nstlog = 500
nstenergy = 100
nstxout = 0
nstvout = 0
nstfout = 0
; Output for xtc file
nstxtcout = 5000
xtc-precision = 1000
; Neighborsearching parameters
nstlist = 5
ns_type = grid
; Temperature coupling
tcoupl = Berendsen
tc_grps = system
tau_t = 0.1
ref_t = 298
; Constraint options
constraints = all-bonds
constraint-algorithm = lincs
unconstrained-start = no
; Relative tolerance of shake
shake-tol = 0.0001
; LINCS parameters
lincs-order = 12
lincs-warnangle = 30
; Periodic boundary conditions
pbc = xyz
; nblist cut-off
rlist = 0.9
; Electrostatics
coulombtype = pme
rcoulomb = 0.9
; vdw cut-off lengths
rvdw = 1.4
; FFT parameters
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; PME parameters
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Generate velocities is on
gen_vel = yes
gen_temp = 298
gen_seed = -1
; Free energy control stuff
free_energy = yes
init_lambda = 0.0
delta_lambda = 0
sc_alpha = 0
sc_power = 1.0
sc_sigma = 0
---end of nvt.mdp file---
---Tail of in vacuo log file---
M E G A - F L O P S A C C O U N T I N G
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces
Computing: M-Number M-Flops % of Flops
-----------------------------------------------------------------------
LJ 0.005001 0.165033 0.0
Free energy innerloop 1.504697 225.704550 0.0
Outer nonbonded loop 0.371929 3.719290 0.0
1,4 nonbonded interactions 0.345069 31.056210 0.0
Spread Q Bspline 20.484096 40.968192 0.0
Gather F Bspline 20.484096 245.809152 0.0
3D-FFT 227370.585024 1818964.680192 90.5
Solve PME 2964.112704 189703.213056 9.4
NS-Pairs 0.078078 1.639638 0.0
Reset In Box 0.032032 0.288288 0.0
Shift-X 0.320064 1.920384 0.0
CG-CoM 0.012012 0.348348 0.0
Angles 0.255051 41.573313 0.0
Propers 0.055011 12.597519 0.0
Impropers 0.135027 28.085616 0.0
Virial 0.385077 6.931386 0.0
Update 0.320064 9.921984 0.0
Stop-CM 0.001600 0.016000 0.0
Calc-Ekin 0.160064 4.321728 0.0
Lincs 0.340136 20.408160 0.0
Lincs-Mat 14.285712 57.142848 0.0
Constraint-Vir 0.170102 4.082448 0.0
-----------------------------------------------------------------------
Total 2009404.593335 100.0
-----------------------------------------------------------------------
NODE (s) Real (s) (%)
Time: 1142.590 1143.000 100.0
19:02
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 0.000 1.759 0.756 31.739
---end of log file---
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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