On 25/10/2011 9:54 AM, Sai Pooja wrote:
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?
Simply moving to double precision will slow things down noticeably. How
much depends on a lot of things, but you can test this yourself with a
non-PLUMED double-precision GROMACS.
Otherwise, you should consider whether whatever you are doing with
PLUMED is expected to take a lot longer than normal...
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)
Those cut-offs do not look like any I've ever seen for CHARMM force
fields. It is not wise to haphazardly choose large values for poor
electrostatic algorithms and hope for the best - even though almost all
force fields were parameterized with poor electrostatic treatments.
Mark
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
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