[gmx-users] Slow in double-precision version
Sai Pooja
saipooja at gmail.com
Tue Oct 25 00:54:13 CEST 2011
Hi all,
I am using GROMACS with the plugin PLUMED in double precision. The
speed has gone down by a huge margin and I was wondering if there is
something in 1) compilation 2) md parameters that could be
contributing to this?
md parameters:
title = NVT simulation (constant number, volume and
temperature)
cpp = /lib/cpp
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.002
nsteps = 5000000
; OUTPUT CONTROL OPTIONS
nstxout = 0 ; ast frame (coordinates)
nstvout = 2000 ; (velocities)
nstfout = 2000 ; No output, except for last frame (forces)
nstlog = 1000 ; Write every step to the log
nstenergy = 1000 ; Write energies at every step
xtc_grps = Protein Non-Protein
nstxtcout = 500 ; Do not write a compressed trajectory
energygrps = Protein SOL ; Write energy information
separately for these groups
;energygrp_table = Protein SOL SOL SOL
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 1.8
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = Cut-off
fourierspacing = 0.15
rcoulomb = 1.8
;rcoulomb_switch = 1.6
epsilon_rf = 78
vdw-type = Cut-off
rvdw = 1.8
;rvdw-switch = 1.6
;table-extension = 1.0
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = no
; Temperature coupling
tcoupl = nose-hoover
tc-grps = Protein Non-Protein
tau_t = 0.4 0.4
ref_t = 300 300
; Pressure coupling
pcoupl = no
; OPTIONS FOR BONDS
constraints = all-bonds
Details of the simulation:
1) MD with explicit solvent using charmm27 with tip3p (recommended one)
2) gromacs 4.5.1
3) With plumed
4) Double precision
5) Position restraints for some parts of the protein (5 chains)
I would really appreciate any help.
Regards
Pooja
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
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