On 25/10/2011 3:11 PM, Sai Pooja wrote:
Thank you so much Mark. You are right about the cut-off values. I am
now using 1.2nm which appears more commonly in literature. If possible
please take a look at these statistics:
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Neighbor search 1 380527 166719.792 59692.7 2.3
Force 1 3805262 1068307.182 382498.9 14.8
Write traj. 1 10433 1319.463 472.4 0.0
Update 1 3805262 12043.902 4312.2 0.2
Constraints 1 3805262 18769.536 6720.3 0.3
Rest 1 5965690.942 2135968.4 82.5
-----------------------------------------------------------------------
Total 1 7232850.817 2589664.9 100.0
-----------------------------------------------------------------------
NODE (s) Real (s) (%)
Time: 2476509.010 2589664.940 95.6
28d15h55:09
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 16.281 468.817 0.266 90.391
Finished mdrun on node 0 Thu Oct 13 21:43:03 2011
It seems like "Rest" option is taking 82% time. Now would this
correspond to an external program like plumed
Yep. "rest" is a catch-all, and plumed is probably not anywhere else.
Their developers would be able to tell you.
Mark
or is it something else?
Regards
Pooja
On Mon, Oct 24, 2011 at 8:18 PM, Mark Abraham<mark.abra...@anu.edu.au> wrote:
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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