[gmx-users] Slow in double-precision version

[Sai Pooja]

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.